XB-FEAT-876285: Difference between revisions
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=nomenclature changes to keratin gene family= | =nomenclature changes to keratin gene family= | ||
10/8/2018 | 10/8/2018 | ||
Following an extensive assessment of the keratin gene family during annotation for X. laevis v 9.1 genome, Xenbase genome curators have made nomenclature updates for Xenopus keratin genes. The data analysis for all gene name changes include synteny analyses (which involves aligning with human and other species genomes, assessing sequence conservation, gene order, neighboring genes, location on chromosome), and identifying the number of duplications (if any) in the X laevis S and L chromosomes, and then applying standardized gene nomenclature rules. For example, genes that have been determined to be copies or tandem duplications are sequentially numbered (ie, gene 1 gene 2, gene 3, etc.) and the gene symbol has a ‘point’ then the gene number such as krt12.5 (pronounced “k r t twelve point five”). Not all genes are found in both X. tropicalis and X. laevis, e.g. krt61 is on chromosome 2 in X. tropicalis and on Chromosome 2 in the X laevis.L, but it does not occur on X. laevis.S. | Following an extensive assessment of the keratin gene family during annotation for X. laevis v 9.1 genome, Xenbase genome curators have made nomenclature updates for Xenopus keratin genes. The data analysis for all gene name changes include synteny analyses (which involves aligning with human and other species genomes, assessing sequence conservation, gene order, neighboring genes, location on chromosome), and identifying the number of duplications (if any) in the X laevis S and L chromosomes, and then applying standardized gene nomenclature rules. For example, genes that have been determined to be copies or tandem duplications are sequentially numbered (ie, gene 1 gene 2, gene 3, etc.) and the gene symbol has a ‘point’ then the gene number such as krt12.5 (pronounced “k r t twelve point five”). Not all genes are found in both X. tropicalis and X. laevis, e.g. krt61 is on chromosome 2 in X. tropicalis and on Chromosome 2 in the X laevis.L, but it does not occur on X. laevis.S. | ||
Full nomenclature rules are accessible via a link on the Xenbase home page. | Full nomenclature rules are accessible via a link on the Xenbase home page. | ||
The following changes have been made in the database and are reflected on Xenbase gene pages: | The following changes have been made in the database and are reflected on Xenbase gene pages: | ||
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keratin 5, gene 4 (krt5.4) renamed keratin 78 gene 7 (krt78.7) | keratin 5, gene 4 (krt5.4) renamed keratin 78 gene 7 (krt78.7) | ||
keratin 5, gene 5 (krt5.5) renamed keratin 62 (krt62) | keratin 5, gene 5 (krt5.5)(also n=known as xlk and larval keratin renamed keratin 62 (krt62) | ||
keratin 5, gene 7 (krt5.7, also known as xck55 and ck55) renamed keratin 7 (krt7) | keratin 5, gene 7 (krt5.7, also known as xck55 and ck55) renamed keratin 7 (krt7) | ||
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keratin 5.6 renamed keratin 78 gene 2 ( krt78.2) | keratin 5.6 renamed keratin 78 gene 2 ( krt78.2) | ||
63kDa Keratin renamed keratin 78, gene 6 ( krt78.6) | keratin 6 (krt6) (also known as 63kDa Keratin, adult keratin and pUF164) was renamed keratin 78, gene 6 ( krt78.6) | ||
krt6a renamed keratin 78, gene 5 ( krt78.5) | krt6a renamed keratin 78, gene 5 ( krt78.5) | ||
krt8 renamed keratin 8, gene 1 ( krt8.1) | krt8 renamed keratin 8, gene 1 ( krt8.1) | ||
xak-a renamed keratin 51 ( krt51) | keratin24 (krt24 (also known as xak-a) was renamed keratin 51 ( krt51) | ||
krt14 ( also known as ck14, nfj and ebs3) | krt14 ( also known as ck14, nfj and ebs3) was renamed keratin 12 gene 1 (krt12.1) | ||
fin and gill keratin (krt16 ) was renamed keratin 12 gene 2 (krt12.2) | fin and gill keratin (krt16 ) was renamed keratin 12 gene 2 (krt12.2) | ||
larval keratin renamed keratin | keratin12 (krt12, also known as xk81b2 and larval keratin) was renamed keratin 12, gene 5 ( krt12.5) | ||
adult specific keratin (as known as xak-c) was renamed keratin 12 gene 6 ( krt12.6) | adult specific keratin (as known as xak-c) was renamed keratin 12 gene 6 ( krt12.6) | ||
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krt10 was renamed keratin 50 (krt50) | krt10 was renamed keratin 50 (krt50) | ||
krt18a was renamed keratin 18 gene 1 ( krt18.1) | krt18a (also known as krt18, endo-b-keratin, k18 and cyk18) was renamed keratin 18 gene 1 ( krt18.1) | ||
LOC100036883 was renamed keratin 20 (krt20) | LOC100036883 was renamed keratin 20 (krt20) | ||
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keratin 35 was renamed keratin 34 (krt34) | keratin 35 was renamed keratin 34 (krt34) | ||
krt-b was renamed keratin 780 (krt70) | |||
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keratin 78 gene 3, (krt 78.3) | keratin 78 gene 3, (krt 78.3) | ||
keratin 78 gene (krt78.4) | keratin 78 gene 4 (krt78.4) | ||
keratin 78 gene 9 (krt78.9) | keratin 78 gene 9 (krt78.9), named changed from krt79, krt79.2 | ||
keratin-like (krt-like) | keratin-like (krt-like) | ||
Latest revision as of 08:00, 23 July 2019
krt59
This is the community wiki page for the gene krt59 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
10/8/2019
Xenopus gene name and gene symbol for keratin 5, gene 3 (krt5.3) was changed to keratin 59 (krt59)
nomenclature changes to keratin gene family
10/8/2018 Following an extensive assessment of the keratin gene family during annotation for X. laevis v 9.1 genome, Xenbase genome curators have made nomenclature updates for Xenopus keratin genes. The data analysis for all gene name changes include synteny analyses (which involves aligning with human and other species genomes, assessing sequence conservation, gene order, neighboring genes, location on chromosome), and identifying the number of duplications (if any) in the X laevis S and L chromosomes, and then applying standardized gene nomenclature rules. For example, genes that have been determined to be copies or tandem duplications are sequentially numbered (ie, gene 1 gene 2, gene 3, etc.) and the gene symbol has a ‘point’ then the gene number such as krt12.5 (pronounced “k r t twelve point five”). Not all genes are found in both X. tropicalis and X. laevis, e.g. krt61 is on chromosome 2 in X. tropicalis and on Chromosome 2 in the X laevis.L, but it does not occur on X. laevis.S.
Full nomenclature rules are accessible via a link on the Xenbase home page.
The following changes have been made in the database and are reflected on Xenbase gene pages:
keratin 5, gene 1 (krt5.1, pUF23) was renamed keratin 78 gene 8 (krt78.8)
keratin 5, gene 2 (krt5, krt5.2) renamed keratin 61 (krt61)
keratin 5, gene 3 ( krt5.3) renamed keratin 59 (krt59)
keratin 5, gene 4 (krt5.4) renamed keratin 78 gene 7 (krt78.7)
keratin 5, gene 5 (krt5.5)(also n=known as xlk and larval keratin renamed keratin 62 (krt62)
keratin 5, gene 7 (krt5.7, also known as xck55 and ck55) renamed keratin 7 (krt7)
keratin 75 (krt75) was renamed keratin 78 gene 1 (krt78.1)
keratin 5.6 renamed keratin 78 gene 2 ( krt78.2)
keratin 6 (krt6) (also known as 63kDa Keratin, adult keratin and pUF164) was renamed keratin 78, gene 6 ( krt78.6)
krt6a renamed keratin 78, gene 5 ( krt78.5)
krt8 renamed keratin 8, gene 1 ( krt8.1)
keratin24 (krt24 (also known as xak-a) was renamed keratin 51 ( krt51)
krt14 ( also known as ck14, nfj and ebs3) was renamed keratin 12 gene 1 (krt12.1)
fin and gill keratin (krt16 ) was renamed keratin 12 gene 2 (krt12.2)
keratin12 (krt12, also known as xk81b2 and larval keratin) was renamed keratin 12, gene 5 ( krt12.5)
adult specific keratin (as known as xak-c) was renamed keratin 12 gene 6 ( krt12.6)
krt5.L (also known as xak-b) was renamed keratin 55 (krt55)
krt10 was renamed keratin 50 (krt50)
krt18a (also known as krt18, endo-b-keratin, k18 and cyk18) was renamed keratin 18 gene 1 ( krt18.1)
LOC100036883 was renamed keratin 20 (krt20)
keratin 13 ( also known as k13 and ck13) was renamed keratin 15, gene 1 (krt15.1)
xlk2 was renamed keratin 15 type 1 gene 2 (krt15.2)
keratin 35 was renamed keratin 34 (krt34)
krt-b was renamed keratin 780 (krt70)
The following are newly identified keratin genes:
keratin 9, gene 1 (krt9.1)
keratin 9, gene 2 (krt 9.2)
keratin 12, gene 3krt12.3)
keratin 18 gene 2 (krt18.2)
keratin 18 gene 3 (krt18.3)
keratin 23 (krt 23)
keratin 24 (krt 24)
keratin 52 (krt 52)
keratin 53 (krt 53)
keratin 54 (krt 54)
keratin 56 (krt 56)
keratin 57 (krt 57)
keratin 58 (krt 58)
keratin 60 (krt 60)
keratin 78 gene 3, (krt 78.3)
keratin 78 gene 4 (krt78.4)
keratin 78 gene 9 (krt78.9), named changed from krt79, krt79.2
keratin-like (krt-like)