RetrogeneDB ID: | retro_cfam_1426 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 30:39697787..39698569(-) | ||
| Located in intron of: | ENSCAFG00000018100 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BSG | ||
| Ensembl ID: | ENSCAFG00000019717 | ||
| Aliases: | None | ||
| Description: | basigin (Ok blood group) [Source:HGNC Symbol;Acc:1116] |
Retrocopy-Parental alignment summary:
>retro_cfam_1426
GTGGTGCTGGCACAGCTGAGCACTGAGGGCGGCTCTGGGGCAGGGAGCAGGCTCTGGAACTCTGTAGATGATATTGGCTC
CAAAACATGCCTTACCTGCACCTTGAACCATCACGCCACTGAGAGTGTCAGCTACCCGCTGGGTGAAGGGCGGGGGGAGC
AAGTCGCTGAAGGGGGACACATTGCCTGAAGACGGAATATGAGATAGACTTGGATGACCACTCCAGTGAGTACTCATGCA
TCTTCCTCCCAGAACAGGCAGGCAAGACCAGCATTGAAATGAAGGGGCTTCCCAACATCAAGGCCATGAAGTCAGAGCAT
GCCACCGAGGGGAAGACAGTCACGTTGGGCTGTAAGTTGGACTCCTTGCCCCTGGTCAGCAACTGGGTGTGGTACAAGTA
GAAAGCTCCAGGGACCAGGTAATCAGCAACAACTCCCAGAGCAAGTTCTTCATGATGTCCTTGGAGACCAAGAGAGAGCT
GCACATCTCAAACCAGGACCTGGAGGAAGACCCTGGCAAGTATGTCTTCAATGGCACCAACTTGGGAGGGCACCACCAGC
CAGACCATCATTTTGCTGCATGTGCAAAACCGCTCTGCCACCCTCTGGCCCTTCCTGGGTGTTGTGGCCAAGGCACTGGT
GCTGATCACAGTTATTTTCATCTATGAGAAGTGGTGGAAGCCAGACAAGGTCCTGGATGATGATGACATGGGCTTGGCTC
CTCTGAAGGGCAGCAGGCATATGAACACCAAAGGCAAGAACCTTTGCCAGAGGAGGCCCAAC
ORF - retro_cfam_1426 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.3 % |
| Parental protein coverage: | 97.01 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LALALLGAGGGSGAGSEILTSVEDIGSKIRLTCSLNRSTTE-ITGHRWVK--GDRVLKEDTFPD-PKTEY |
| ..LA.L...GGSGAGS....SV.DIGSK..LTC.LN...TE.....RWVK..G...LK.DT.P.....E. | |
| Retrocopy | VVLAQLSTEGGSGAGSRLWNSVDDIGSKTCLTCTLNHHATE>VSATRWVKGGGSKSLKGDTLPE>TEYEI |
| Parental | EVDSDERSGEYSCIFLPELLGKSSIEVRGLPNIKAVKKSEHATERETVVLGCRSDSFPPVTDWVWYK-VE |
| ..D....S.EYSCIFLPE..GK.SIE..GLPNIKA..KSEHATE..TV.LGC..DS.P.V..WVWYK.VE | |
| Retrocopy | DLD--DHSSEYSCIFLPEQAGKTSIEMKGLPNIKAM-KSEHATEGKTVTLGCKLDSLPLVSNWVWYK<VE |
| Parental | SSGDQVISNSSQSKFLVVSSETKTELRISNLDLETDPGKYVCNGTNS-EGT-SQAVIVLRVRNRFAALWP |
| SS.DQVISN.SQSKF...S.ETK.EL.ISN.DLE.DPGKYV.NGTN..EGT.SQ..I.L.V.NR.A.LWP | |
| Retrocopy | SSRDQVISNNSQSKFFMMSLETKRELHISNQDLEEDPGKYVFNGTNL>EGTTSQTIILLHVQNRSATLWP |
| Parental | FLGIVAEVLVLVTVIFIYEKRRKPDEVLDDEDTGSAPLKSSGHVNDKGKNVRQRNAN |
| FLG.VA..LVL.TVIFIYEK..KPD.VLDD.D.G.APLK.S.H.N.KGKN..QR..N | |
| Retrocopy | FLGVVAKALVLITVIFIYEKWWKPDKVLDDDDMGLAPLKGSRHMNTKGKNLCQRRPN |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 227 .55 RPM |
| SRP017611_brain | 0 .00 RPM | 172 .36 RPM |
| SRP017611_kidney | 0 .00 RPM | 1043 .52 RPM |
| SRP017611_liver | 0 .00 RPM | 302 .67 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1426 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1426 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1426 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019717 | 1 retrocopy |
retro_cfam_1426 ,
|
| Felis catus | ENSFCAG00000007837 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000009184 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000006517 | 2 retrocopies | |
| Mustela putorius furo | ENSMPUG00000009950 | 1 retrocopy |