XB-FEAT-954189: Difference between revisions

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Annotated fibrillin genes in representative non-Mammalian eukaryotes.'''
Annotated fibrillin genes in representative non-Mammalian eukaryotes.'''


Key: Species Gene symbol Ensembl ID Position Syntenic human genea
Key: Species Gene symbol Ensembl ID Position Syntenic human gene '''a'''
  Birds
  Birds
''Gallus gallus'' (Chicken reference)
''Gallus gallus'' (Chicken reference)
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FBN2 ENSTGUG00000006641 Z: 19,412,687–19,528,936 FBN2
FBN2 ENSTGUG00000006641 Z: 19,412,687–19,528,936 FBN2


Novel gene fragmentsb ENSTGUG00000000946 ENSTGUG00000022997 ENSTGUG00000023585 ENSTGUG00000025566 28:1,198,218–1,257,990 FBN3
Novel gene fragments '''b''' ENSTGUG00000000946 ENSTGUG00000022997 ENSTGUG00000023585 ENSTGUG00000025566 28:1,198,218–1,257,990 FBN3


  Reptiles
  Reptiles
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FBN2 ENSPSIG00000014580 Scaffold JH211314.1: 448,230–733,300 FBN2
FBN2 ENSPSIG00000014580 Scaffold JH211314.1: 448,230–733,300 FBN2


Novel genec ENSPSIG00000014464 Scaffold JH209348.1: 425,806–425,933 FBN3
Novel gene '''c''' ENSPSIG00000014464 Scaffold JH209348.1: 425,806–425,933 FBN3


''Crocodylus porosus''(Australian salt water crocodile)
''Crocodylus porosus''(Australian salt water crocodile)
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''Danio rerio'' (Zebrafish)
''Danio rerio'' (Zebrafish)


fbn1 ZDB-GENE-091204–466e 18:5,316,207–5,345,282 FBN1
fbn1 ZDB-GENE-091204–466 '''e''' 18:5,316,207–5,345,282 FBN1


fbn2a ENSDARG00000051896 10:16,313,851–16,474,216 FBN2
fbn2a ENSDARG00000051896 10:16,313,851–16,474,216 FBN2
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FBN1 ENSGMOG00000008510 14: 13,478,893–13,542,240 FBN1
FBN1 ENSGMOG00000008510 14: 13,478,893–13,542,240 FBN1


fbn2b ENSGMOG00000009755 12: 26,359,137–26,397,080 [FBN3]f
fbn2b ENSGMOG00000009755 12: 26,359,137–26,397,080 [FBN3]'''f'''


''Salmo salar'' (Atlantic salmon)
''Salmo salar'' (Atlantic salmon)
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Note: Gene annotations and positions taken from Ensembl (Release 110, July 2023; http://www.ensembl.org).
'''Notes: Gene annotations and positions taken from Ensembl (Release 110, July 2023; http://www.ensembl.org).
'''


a Synteny based on presence of at least 2 of the same annotated flanking genes in both species.
'''a''' Synteny based on presence of at least 2 of the same annotated flanking genes in both species.


b Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSGALG00010028301.
'''b''' Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSGALG00010028301.


c Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSCPRG00005013427.
'''c''' Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSCPRG00005013427.


dWhole genome duplication occurred in the ancestor of teleost fishes. Some lineages including the salmonids have undergone subsequent additional whole genome duplication. There has also been extensive genome rearrangement during evolution of the fish lineages, which means that the synteny with the human genome often breaks down. There may eventually have been loss of 1 member of the duplicated gene pair, both pairs may have retained the same function, the function may have been divided between the 2 pairs or 1 pair may have acquired a new function. It is likely that the ancestral teleost had 3 distinct fibrillin genes, corresponding to human FBN1, FBN2, and FBN3. In most species at least 80% of the duplicated genes have subsequently been lost; for the salmonids up to 50% have been retained. This is consistent with the different numbers of fibrillin genes found in fugu and zebrafish when compared with Atlantic salmon. See Glasauer and Neuhauss (2014) for a review. It is also likely that annotation of the homologs and paralogues has been difficult in the fish sequences because of the multiple copies present.
'''d''' Whole genome duplication occurred in the ancestor of teleost fishes. Some lineages including the salmonids have undergone subsequent additional whole genome duplication. There has also been extensive genome rearrangement during evolution of the fish lineages, which means that the synteny with the human genome often breaks down. There may eventually have been loss of 1 member of the duplicated gene pair, both pairs may have retained the same function, the function may have been divided between the 2 pairs or 1 pair may have acquired a new function. It is likely that the ancestral teleost had 3 distinct fibrillin genes, corresponding to human FBN1, FBN2, and FBN3. In most species at least 80% of the duplicated genes have subsequently been lost; for the salmonids up to 50% have been retained. This is consistent with the different numbers of fibrillin genes found in fugu and zebrafish when compared with Atlantic salmon. See Glasauer and Neuhauss (2014) for a review. It is also likely that annotation of the homologs and paralogues has been difficult in the fish sequences because of the multiple copies present.
efbn1 is not annotated in the Ensembl and University of California Santa Cruz (UCSC) browsers but has been annotated in the NCBI Gene database in a position syntenic with human FBN1. The ID given here is the Zebrafish Information Network (ZFIN) accession.
efbn1 is not annotated in the Ensembl and University of California Santa Cruz (UCSC) browsers but has been annotated in the NCBI Gene database in a position syntenic with human FBN1. The ID given here is the Zebrafish Information Network (ZFIN) accession.


f Only 1 matching flanking gene; many unannotated genes in region.
'''f''' Only 1 matching flanking gene; many unannotated genes in region.

Revision as of 07:18, 8 January 2024

fbn1

This is the community wiki page for the gene fbn1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

fibrillin genes in representative non-Mammalian eukaryotes

Source: Genetic models of fibrillinopathies by Kim M Summers, Genetics, Volume 226, Issue 1, January 2024, iyad189, https://doi.org/10.1093/genetics/iyad189

Published: 16 November 2023

Table 5. Annotated fibrillin genes in representative non-Mammalian eukaryotes.

Key: Species Gene symbol Ensembl ID Position Syntenic human gene a 

Birds

Gallus gallus (Chicken reference)

FBN1 ENSGALG00010018446 10: 10,196,204–10,347,306 FBN1

FBN2 ENSGALG00010012940 Z: 57,572,115–57,735,283 FBN2

Novel gene ENSGALG00010028301 28: 748,104–807,082 FBN3

Taeniopygia guttata(Zebra finch)

FBN1 ENSTGUG00000019967 10: 10,687,753–10,833,054 FBN1

FBN2 ENSTGUG00000006641 Z: 19,412,687–19,528,936 FBN2

Novel gene fragments b ENSTGUG00000000946 ENSTGUG00000022997 ENSTGUG00000023585 ENSTGUG00000025566 28:1,198,218–1,257,990 FBN3 

Reptiles

Pelodiscus sinensis (Chinese soft shell turtle)

FBN1 ENSPSIG00000013146 Scaffold JH212494.1: 1,344,550–1,567,396 FBN1

FBN2 ENSPSIG00000014580 Scaffold JH211314.1: 448,230–733,300 FBN2

Novel gene c ENSPSIG00000014464 Scaffold JH209348.1: 425,806–425,933 FBN3

Crocodylus porosus(Australian salt water crocodile)

FBN1 ENSCPRG00005014181 MDVP01000032.1: 22,496,653–22,704,014 FBN1

FBN2 ENSCPRG00005010570 MDVP01000068.1: 10,977,784–11,261,323 FBN2

FBN3 ENSCPRG00005013427 MDVP01000063.1: 4,384,393–4,473,954 FBN3 

Amphibians

Xenopus tropicalis (African Clawed toad)

fbn1 ENSXETG00000008779 3: 103,789,676–103,911,959 FBN1

fbn2 ENSXETG00000032535 1: 167,581,240–167,726,912 FBN2

fbn3 ENSXETG00000001781 1: 92,395,786–92,500,369 FBN3 

Fish

Takifugu rubripes (Fugu)

fbn2b ENSTRUG00000012996 20: 9,649,309–9,687,408 FBN3

Danio rerio (Zebrafish)

fbn1 ZDB-GENE-091204–466 e 18:5,316,207–5,345,282 FBN1

fbn2a ENSDARG00000051896 10:16,313,851–16,474,216 FBN2

fbn2b ENSDARG00000098237 22:4,524,367–4,649,238 FBN3

Gadus morhua (Atlantic cod) FBN1 ENSGMOG00000008510 14: 13,478,893–13,542,240 FBN1

fbn2b ENSGMOG00000009755 12: 26,359,137–26,397,080 [FBN3]f

Salmo salar (Atlantic salmon)

FBN1 ENSSSAG00000097601 11: 32,338,996–32,703,955 FBN1

FBN1 ENSSSAG00000095019 26:32,713,409–32,886,730 FBN1 [clearly needs nomenclature attention]

fbn2a NSSSAG00000077250 1:166,160,786–166,373,162 FBN2

fbn2b ENSSSAG00000007909 10:19,346,980–19,436,215 FBN3

fbn2b ENSSSAG00000057875 16:39,779,019–39,904,486

Scleropages formosus (Asian bonytongue)

FBN1 ENSSFOG00015017770 7: 31,324,447–31,376,124 FBN1

FBN1 ENSSFOG00015013164 11: 11,118,508–11,169,624 FBN1

fbn2a ENSSFOG00015007953 6: 13,440,703–13,514,547 FBN2

fbn2b ENSSFOG00015006450 9: 832,842–881,796 FBN3 

Insects

Apis mellifera (Honey bee)

LOC409950 CM009932.2:639479–663432 FBN1

LOC100577456 CM009941.2:11397504–11424515 FBN2

LOC724421 CM009945.2:5255226–5265494 FBN2

LOC725800 CM009936.2:4978223–5138349 FBN2 

Nematode

Caenorhabditis elegans fbn-1 WBGene00022816 Chromosome III: 7,625,386–7,641,078 fibrillins

mua-3 WBGene00003482 Chromosome III: 10,160,697–10,183,529 fibrillins


Notes: Gene annotations and positions taken from Ensembl (Release 110, July 2023; http://www.ensembl.org).

a Synteny based on presence of at least 2 of the same annotated flanking genes in both species.

b Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSGALG00010028301.

c Detected by performing TBLASTN search in Ensembl using the protein sequence derived from ENSCPRG00005013427.

d Whole genome duplication occurred in the ancestor of teleost fishes. Some lineages including the salmonids have undergone subsequent additional whole genome duplication. There has also been extensive genome rearrangement during evolution of the fish lineages, which means that the synteny with the human genome often breaks down. There may eventually have been loss of 1 member of the duplicated gene pair, both pairs may have retained the same function, the function may have been divided between the 2 pairs or 1 pair may have acquired a new function. It is likely that the ancestral teleost had 3 distinct fibrillin genes, corresponding to human FBN1, FBN2, and FBN3. In most species at least 80% of the duplicated genes have subsequently been lost; for the salmonids up to 50% have been retained. This is consistent with the different numbers of fibrillin genes found in fugu and zebrafish when compared with Atlantic salmon. See Glasauer and Neuhauss (2014) for a review. It is also likely that annotation of the homologs and paralogues has been difficult in the fish sequences because of the multiple copies present. efbn1 is not annotated in the Ensembl and University of California Santa Cruz (UCSC) browsers but has been annotated in the NCBI Gene database in a position syntenic with human FBN1. The ID given here is the Zebrafish Information Network (ZFIN) accession.

f Only 1 matching flanking gene; many unannotated genes in region.

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