RetrogeneDB ID: | retro_ecab_501 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 2:89814663..89817355(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000003426 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LPIN2 | ||
| Ensembl ID: | ENSECAG00000006280 | ||
| Aliases: | None | ||
| Description: | lipin 2 [Source:HGNC Symbol;Acc:14450] |
Retrocopy-Parental alignment summary:
>retro_ecab_501
ATGAATTATGTGGGACAGCTGGCTGGGCAGGTGATTGTCACTGTGAAAGAACTCTACAAAGGCGTTAACCAAGCCACTCT
GTCCGGGTGCATCGATGTCATTGTGGTACGGCAGCAGGATGGCACCTATCAGTGTTCGCCATTTCAGGTTCGGTTCGGGA
AGCTGGGAGTCCTGAGATCCAAGGAGAAAGTGATTGATATAGAAATCAATGGCGATGCAGTGGATCTTCACATGAAATTG
GGTGACAATGGAGAAGCTTTCTTTGTGGAGGAGACTGAAGAGGAATATGAAAAGCTTCCTGCTTACCTTGCCACCTCACC
AATTCCTACTGAAGATCACTTCTTCAAAGATATTGACACCCGTTTTGTGAAATCTGGTGGAAATGAAAGACCATCTCAGA
GTTCAGACATCTCACACATCTTGGACACGGAGAGAGATTTTGCTCCAAGTTCTGTGAAAAAGAAAAAACAAAGGACAAAG
AAATGCAAACAGGACAGTAAGAAGGAAGACCAGGCCACTTGCCCTGCTGCAGAGGACACCGTGGATGTGAACCTGAGTTC
TGACGATGGCAAGGGGGCCCAGTCAGCAAGAGGATCTTCAAATGCTTCCTTAAAGGAAGAAGAATATAAAGAGCCTTTGC
TTTTCCATTCTGGGGATCAATACTCCTTATCTGATGGAGACTGGTCGCCTTCAGACAACACCTATTCCCCAAGGGCAGTG
TGTCCTAAGAGCGATTCAGAGCTGGAGGTGAAACCAGCCGAGAGCCTGCTCAGATCTGAGTCCCACATGGAGTGGACGTG
GGGCGGGTTCCCACAGTCCACCAAGGTCAGCAAAAGAGACAGATCTGACCATCATCCTAGGACAGGTACGATTACACCAT
CAGAAAATACCCATTTTCGGGTAATTTCAAGTGAGGACAGGCTCAGCAGTGAGGTTGAAAAGGATGCTTCCATGGGAGAA
ACGGTCTGTACCATAGTGAAACCCAAACCCAGAGCCCTGTGTAAGCAGATGAGCGATGCAACTAGAGCTGCAGGACTTGT
CGAACCTCTCCTTGAGCCACCTCCGATTTCATCTATGTTAGATGCAGACCACCTTCCCAACCCCTCGTTGCTGGAGGCTC
CCTCAGAATCAAAACCAGCAGCTAAGGTAGACTCGCCGTCAAAGAAGAAAGGTGTCCACAAGAGAAGCCAACACCAGGGA
CCTGATGATATTTACCTAGATGATTTAAAGGCTCTAGAACCTGAAGTCGCAGCTCTCTGTTTCCCTAAAAGTGGATCAGA
CCCCGTCTCCAGGCAGTGACCCGAGTCTGACACGCCTTCTGGCTCCCAGTCCCCGCAGTCCGTGGGAAGCGCGGCCACTG
ATAGTGGCACTGAGTGCCTCTTGGATTCTACCATGGACTTGCCCGACGTCACCCTCTCCCTTTGTGGGGGCCTCAGTGAG
AATGGAGAAATTTCTAAAGAAAAATTCGTGGAGCATATCATTACTTATCATGAATTTGCAGAAAACCCTGGACTTATAGA
CAATCCTAACCTTGTAATACGGATATATAACCGTTACTATAACTGGGCTTTGGCTGCTCCCATGATCCTTAGCTTACAAG
TGTTCCAGAAGAGCTTGCCTAAGGCCTCAGTCGAGTCCTGGGTCAAAGATAAGATGCCAAAGAAATCTGGTCGCTGGTGG
TTTTGGCGTAAGAGAGAAAGCATGACCAAACAGCTGCCGGAGGCCAAGGAAGGGAAATCCGAGGTGCTTGCCGACGAGTG
ACCTGCCGTCAGGTGCAAAGGAGCTGGCCAGTGGCAGGTCAGCCGAGGATGACTCGTCGAGTGACGAGGGATCACAGGAG
CTCGAAGAATCAATCAAAGTGGACCCCGTCCCCACAGAGCCCCCGAGCCACGGCAGCACGACCTCATATAAGAAGTCTCT
TCAACTCTCCTCAGACCAGATTGCAAAACTGAAGCTCCAAGATGGCCCAAATGATGTTGTGTTTAGTATTACAACCCAGT
ATCAAGGTACCTGCCGTTGCGCAGGGACCATTTACCTGTGGAACTGGAATGACAAGGTCATCATTTCAGATATCGATGGA
ACGATAATCAAGTCTGATGCTTTGGGACAGATTCTTCCACAGCTGGGTAAAGACTGGACTCATCAGGGTATAGCAAAGCT
CTACCATTCCATCAACAAGAATGGCCACAAGTTTCTGTACTGTTCAGCTTGTGCCATCAGCACGGCTGACGTGACCTGTG
GCTACCTGCACTGAGTCAATGACAAGGGCACAATCTTGCCCCGGGGCCCTCTGATGCTGTCCCCCAGCAGCTTGTTCTCG
GCCTTCCACAGGGAAGTGATAGAAAAGAAACCAGAGAAGTTCAAAATTGAGTGTCTGAATGACATCAAGAATCTGTTTGC
CCCGTCTAAGCAGCCCTTCTATGCTGCCTTTGGAAACCGTCCCAGTGATGTCTATGCTTACACACAAGTTGGAGTTCCAG
ACTGCAGAATATTCACTGTGAACCCCAAGGGTGAATTAATACAAGAAAGGACCAAAGGAAACAAGTCATTGTATCACAGA
CTGAGCGAGCTCGTGGAGCATGTATTCCCACTCCTCAGTAAGGAACAGAATTCCGCATGTCCGTGCCCAGAGTTCAGCTC
CTTCTGCTACTGGCGAGACCCGATCCCCAAAGTGGACCTGGATGACCTGGCC
ORF - retro_ecab_501 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.21 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNYVGQLAGQVIVTVKELYKGINQATLSGCIDVIVVRQQDGTYQCSPFHVRFGKLGVLRSKEKVIDIEIN |
| MNYVGQLAGQVIVTVKELYKG.NQATLSGCIDVIVVRQQDGTYQCSPF.VRFGKLGVLRSKEKVIDIEIN | |
| Retrocopy | MNYVGQLAGQVIVTVKELYKGVNQATLSGCIDVIVVRQQDGTYQCSPFQVRFGKLGVLRSKEKVIDIEIN |
| Parental | GDAVDLHMKLGDNGEAFFVEETEEEYEKLPAYLATSPIPTEDQFFKDIDTRLVKSGGNERPSQSSDISHI |
| GDAVDLHMKLGDNGEAFFVEETEEEYEKLPAYLATSPIPTED.FFKDIDTR.VKSGGNERPSQSSDISHI | |
| Retrocopy | GDAVDLHMKLGDNGEAFFVEETEEEYEKLPAYLATSPIPTEDHFFKDIDTRFVKSGGNERPSQSSDISHI |
| Parental | LDTERVFAPSSVKKKKRRRKKCKQDSKKEDQATCPAAEDTVDVNLSSDDDKGAQSARGSSNASLKEEEYK |
| LDTER.FAPSSVKKKK.R.KKCKQDSKKEDQATCPAAEDTVDVNLSSDD.KGAQSARGSSNASLKEEEYK | |
| Retrocopy | LDTERDFAPSSVKKKKQRTKKCKQDSKKEDQATCPAAEDTVDVNLSSDDGKGAQSARGSSNASLKEEEYK |
| Parental | EPLLFHSGDHYPLSDGDWSPLDNAYSPTAVCPKSDSELEVKPAESLLRSESHMEWTWGGFPESTKVSKRD |
| EPLLFHSGD.Y.LSDGDWSP.DN.YSP.AVCPKSDSELEVKPAESLLRSESHMEWTWGGFP.STKVSKRD | |
| Retrocopy | EPLLFHSGDQYSLSDGDWSPSDNTYSPRAVCPKSDSELEVKPAESLLRSESHMEWTWGGFPQSTKVSKRD |
| Parental | RSDHHPRTATITPSENTHFRVIPSEDSLSSEVEKDASMGETVCTIVKPKPRALCKQMSDATRGAGLVEPL |
| RSDHHPRT.TITPSENTHFRVI.SED.LSSEVEKDASMGETVCTIVKPKPRALCKQMSDATR.AGLVEPL | |
| Retrocopy | RSDHHPRTGTITPSENTHFRVISSEDRLSSEVEKDASMGETVCTIVKPKPRALCKQMSDATRAAGLVEPL |
| Parental | LEPPPISSMLDADQLPNPLLLEAPSESKPAAKVDSPSKKKGVHKRSQHQGPDDIYLDDLKALEPEVAALY |
| LEPPPISSMLDAD.LPNP.LLEAPSESKPAAKVDSPSKKKGVHKRSQHQGPDDIYLDDLKALEPEVAAL. | |
| Retrocopy | LEPPPISSMLDADHLPNPSLLEAPSESKPAAKVDSPSKKKGVHKRSQHQGPDDIYLDDLKALEPEVAALC |
| Parental | FPKSESDPVSRQWPESDTPSGSQSPQSVGSAAADSGTECLLDSTMDLPDVTLSLCGGLSENGEISKEKFM |
| FPKS.SDPVSRQ.PESDTPSGSQSPQSVGSAA.DSGTECLLDSTMDLPDVTLSLCGGLSENGEISKEKF. | |
| Retrocopy | FPKSGSDPVSRQ*PESDTPSGSQSPQSVGSAATDSGTECLLDSTMDLPDVTLSLCGGLSENGEISKEKFV |
| Parental | EHIITYHEFAENPGLIDNPNLVIRIYNRYYNWALAAPMILSLQVFQKSLPKATVESWVKDKMPKKSGRWW |
| EHIITYHEFAENPGLIDNPNLVIRIYNRYYNWALAAPMILSLQVFQKSLPKA.VESWVKDKMPKKSGRWW | |
| Retrocopy | EHIITYHEFAENPGLIDNPNLVIRIYNRYYNWALAAPMILSLQVFQKSLPKASVESWVKDKMPKKSGRWW |
| Parental | FWRKRESMTKQLPEAKEGKSEV-LPTSDLPSGAKEPASGRSAEDDSSSDEGSQELEESIKVDPVPTEPPS |
| FWRKRESMTKQLPEAKEGKSEV.LPTSDLPSGAKE.ASGRSAEDDSSSDEGSQELEESIKVDPVPTEPPS | |
| Retrocopy | FWRKRESMTKQLPEAKEGKSEV>LPTSDLPSGAKELASGRSAEDDSSSDEGSQELEESIKVDPVPTEPPS |
| Parental | HSGTTSYKKSLRLSSDQIAKLKLQDGPNDVVFSITTQYQGTCRCAGTIYLWNWNDKVIISDIDGTITKSD |
| H..TTSYKKSL.LSSDQIAKLKLQDGPNDVVFSITTQYQGTCRCAGTIYLWNWNDKVIISDIDGTI.KSD | |
| Retrocopy | HGSTTSYKKSLQLSSDQIAKLKLQDGPNDVVFSITTQYQGTCRCAGTIYLWNWNDKVIISDIDGTIIKSD |
| Parental | ALGQILPQLGKDWTHQGIAKLYHSINENGYKFLYCSARAIGMADMTRGYLHWVNDKGTILPRGPLMLSPS |
| ALGQILPQLGKDWTHQGIAKLYHSIN.NG.KFLYCSA.AI..AD.T.GYLH.VNDKGTILPRGPLMLSPS | |
| Retrocopy | ALGQILPQLGKDWTHQGIAKLYHSINKNGHKFLYCSACAISTADVTCGYLH*VNDKGTILPRGPLMLSPS |
| Parental | SLFSAFHREVIEKKPEKFKIECLNDIKNLFAPSKQPFYAAFGNRPNDVYAYTQVGVPDCRIFTVNPKGEL |
| SLFSAFHREVIEKKPEKFKIECLNDIKNLFAPSKQPFYAAFGNRP.DVYAYTQVGVPDCRIFTVNPKGEL | |
| Retrocopy | SLFSAFHREVIEKKPEKFKIECLNDIKNLFAPSKQPFYAAFGNRPSDVYAYTQVGVPDCRIFTVNPKGEL |
| Parental | IQERTKGNKSSYHRLSELVEHVFPLLSKEQNSAFPCPEFSSFCYWRDPIPKVDLDDLA |
| IQERTKGNKS.YHRLSELVEHVFPLLSKEQNSA.PCPEFSSFCYWRDPIPKVDLDDLA | |
| Retrocopy | IQERTKGNKSLYHRLSELVEHVFPLLSKEQNSACPCPEFSSFCYWRDPIPKVDLDDLA |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .18 RPM | 16 .59 RPM |
| SRP021940_cerebellum | 0 .57 RPM | 48 .04 RPM |
| SRP021940_embryo | 0 .28 RPM | 46 .36 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 17 .08 RPM |
| SRP021940_synovial_membrane | 0 .11 RPM | 28 .82 RPM |
| SRP021940_testis | 0 .13 RPM | 26 .41 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_501 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_501 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_501 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000006280 | 1 retrocopy |
retro_ecab_501 ,
|