XB-FEAT-5884185: Difference between revisions
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=synteny across vertebrates for DDR1/DDR22/DDR2L= | =synteny across vertebrates for DDR1/DDR22/DDR2L= | ||
The synteny is rather variable for both genes and IER3-like and TUBB-like genes appear in both gene blocks but the aa and nt trees support the orthology. | The synteny is rather variable for both genes and IER3-like and TUBB-like genes appear in both gene blocks but the aa and nt trees support the orthology. | ||
The true DDR1 gene consistently sits between IER3 and GTF2H4 in mammals (eg, Hs NP_001945): | The true DDR1 gene consistently sits between IER3 and GTF2H4 in mammals (eg, Hs NP_001945): | ||
TUBB> FLOT1< IER3< DDR1> GTF2H4> VARS2> SFTA2< | TUBB> FLOT1< IER3< DDR1> GTF2H4> VARS2> SFTA2< | ||
amphibians have one-sided synteny (eg, Xtrop XP_002939505.1): | amphibians have one-sided synteny (eg, Xtrop XP_002939505.1): | ||
TUBB> FLOT1< IER3< DDR1> GNL1< ABCF1> | TUBB> FLOT1< IER3< DDR1> GNL1< ABCF1> | ||
squamates are crazy but TUBB or FLOT1 is generally nearby: | squamates are crazy but TUBB or FLOT1 is generally nearby: | ||
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turtles: | turtles: | ||
TUBB> FLOT1< IER3< DDR1> xnf7> xnf7> | TUBB> FLOT1< IER3< DDR1> xnf7> xnf7> | ||
crocodiles are crazy. Their DDR1 gene is usually on a small, unplaced scaffold (eg, XP_006268561.2) | crocodiles are crazy. Their DDR1 gene is usually on a small, unplaced scaffold (eg, XP_006268561.2) | ||
in birds the region is usually poorly assembled but DDR1 often sits next to IER3 or GTF2H4 (eg, Gg ): | in birds the region is usually poorly assembled but DDR1 often sits next to IER3 or GTF2H4 (eg, Gg ): | ||
vars2< GTF2H4> DDR1> IER3> zfp< | vars2< GTF2H4> DDR1> IER3> zfp< | ||
DDR1 synteny breaks down outside of tetrapods: | DDR1 synteny breaks down outside of tetrapods: | ||
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SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< ENTPD2L< | SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< ENTPD2L< | ||
turtles (eg, XP_043386668): | turtles (eg, XP_043386668): | ||
SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< NPDC1> | SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< NPDC1> | ||
squamates (eg, XP_028570562): | squamates (eg, XP_028570562): | ||
SCAI< RPL35> LOC> TOR4A> DDR2L> NOXA1> ENTPD8< NSMF< | SCAI< RPL35> LOC> TOR4A> DDR2L> NOXA1> ENTPD8< NSMF< | ||
amphibians vary a lot but examples include: | amphibians vary a lot but examples include: | ||
RNF208< RNF224> TOR4A> DDR2L> glipr2> LOC> TPRN> SSNA1< ANAPC2> | RNF208< RNF224> TOR4A> DDR2L> glipr2> LOC> TPRN> SSNA1< ANAPC2> | ||
RNF208< CYSRT1> TOR4A> IER3> DDR2L> glipr2>>> clec/cd209< CCN1L> | RNF208< CYSRT1> TOR4A> IER3> DDR2L> glipr2>>> clec/cd209< CCN1L> | ||
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RNF208< LOC>> TOR4A> IER3> DDR2L> LOC> ccn1l> | RNF208< LOC>> TOR4A> IER3> DDR2L> LOC> ccn1l> | ||
coelacanth: | coelacanth: | ||
RNF208< gaps TOR4A> ier3> DDR2L> GLIPR2> TUBB4B> FAM166A< | RNF208< gaps TOR4A> ier3> DDR2L> GLIPR2> TUBB4B> FAM166A< | ||
gar (assembly has many gaps) | gar (assembly has many gaps) | ||
rnf> TOR4A> DDR2L> glipr2> tubb4b> FAM166A< | rnf> TOR4A> DDR2L> glipr2> tubb4b> FAM166A< | ||
zebrafish | zebrafish | ||
LOC> wdr31> rnf223> TOR4Ab> ier3> DDR2L> pheta1> SH2B3> GAK>//TUBB4B// //TOR4AA// | LOC> wdr31> rnf223> TOR4Ab> ier3> DDR2L> pheta1> SH2B3> GAK>//TUBB4B// //TOR4AA// | ||
great white shark XP_041050061.1 | great white shark XP_041050061.1 | ||
RNF208< TOR4A> DDR2L> glipr2>>>> // | RNF208< TOR4A> DDR2L> glipr2>>>> // | ||
thorny skate XP_032904930 | thorny skate XP_032904930 | ||
MAN1BL> DPP7< tesk2> TNC< DDR2L> glipr2>>> tubb4b>> NOXA1< LOC< EXD3< | MAN1BL> DPP7< tesk2> TNC< DDR2L> glipr2>>> tubb4b>> NOXA1< LOC< EXD3< | ||
monotremes lose the DDR2L gene from this region: | monotremes lose the DDR2L gene from this region: | ||
MAN1B1> DPP7< tesk2> TOR4A> STPG3< FAM166A> TUBB4B< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1< | MAN1B1> DPP7< tesk2> TOR4A> STPG3< FAM166A> TUBB4B< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1< | ||
marsupial and placental mammals also lack DDR2L in this region: | marsupial and placental mammals also lack DDR2L in this region: | ||
ENTPD8> NOXA1< EXD3> NRARP> TOR4A< NELFB< STPG3< FAM166A> TUBB4B< SLC34A3< RNF224< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1< | ENTPD8> NOXA1< EXD3> NRARP> TOR4A< NELFB< STPG3< FAM166A> TUBB4B< SLC34A3< RNF224< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1< | ||
Revision as of 07:33, 9 February 2023
ddr2l
This is the community wiki page for the gene ddr2l please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
synteny across vertebrates for DDR1/DDR22/DDR2L
The synteny is rather variable for both genes and IER3-like and TUBB-like genes appear in both gene blocks but the aa and nt trees support the orthology.
The true DDR1 gene consistently sits between IER3 and GTF2H4 in mammals (eg, Hs NP_001945):
TUBB> FLOT1< IER3< DDR1> GTF2H4> VARS2> SFTA2<
amphibians have one-sided synteny (eg, Xtrop XP_002939505.1):
TUBB> FLOT1< IER3< DDR1> GNL1< ABCF1>
squamates are crazy but TUBB or FLOT1 is generally nearby:
turtles: TUBB> FLOT1< IER3< DDR1> xnf7> xnf7>
crocodiles are crazy. Their DDR1 gene is usually on a small, unplaced scaffold (eg, XP_006268561.2)
in birds the region is usually poorly assembled but DDR1 often sits next to IER3 or GTF2H4 (eg, Gg ):
vars2< GTF2H4> DDR1> IER3> zfp<
DDR1 synteny breaks down outside of tetrapods:
Synteny of DDR2L is also erratic but the gene usually sits downstream of TOR4A and often upstream of FAM166A (eg, Gg NP_001012818):
SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< ENTPD2L<
turtles (eg, XP_043386668):
SSNA1< ANAPC2> TOR4A> DDR2L> FAM166A> TUBB4B< NPDC1>
squamates (eg, XP_028570562): SCAI< RPL35> LOC> TOR4A> DDR2L> NOXA1> ENTPD8< NSMF<
amphibians vary a lot but examples include:
RNF208< RNF224> TOR4A> DDR2L> glipr2> LOC> TPRN> SSNA1< ANAPC2>
RNF208< CYSRT1> TOR4A> IER3> DDR2L> glipr2>>> clec/cd209< CCN1L>
SSNA1< ANAPC2> TOR4A> DDR2L> glipr2> MEGF9> cdk5rap2>
RNF208< LOC>> TOR4A> IER3> DDR2L> LOC> ccn1l>
coelacanth:
RNF208< gaps TOR4A> ier3> DDR2L> GLIPR2> TUBB4B> FAM166A<
gar (assembly has many gaps)
rnf> TOR4A> DDR2L> glipr2> tubb4b> FAM166A<
zebrafish
LOC> wdr31> rnf223> TOR4Ab> ier3> DDR2L> pheta1> SH2B3> GAK>//TUBB4B// //TOR4AA//
great white shark XP_041050061.1
RNF208< TOR4A> DDR2L> glipr2>>>> //
thorny skate XP_032904930
MAN1BL> DPP7< tesk2> TNC< DDR2L> glipr2>>> tubb4b>> NOXA1< LOC< EXD3<
monotremes lose the DDR2L gene from this region:
MAN1B1> DPP7< tesk2> TOR4A> STPG3< FAM166A> TUBB4B< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1<
marsupial and placental mammals also lack DDR2L in this region:
ENTPD8> NOXA1< EXD3> NRARP> TOR4A< NELFB< STPG3< FAM166A> TUBB4B< SLC34A3< RNF224< CYSRT1< RNF208> NDOR1< TPRN> SSNA1< ANAPC2> LRRC26> GRIN1<