RetrogeneDB ID: | retro_amel_253 | ||
Retrocopy location | Organism: | Panda (Ailuropoda melanoleuca) | |
| Coordinates: | GL192366.1:919856..921100(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIMA1 | ||
| Ensembl ID: | ENSAMEG00000001243 | ||
| Aliases: | None | ||
| Description: | LIM domain and actin binding 1 [Source:HGNC Symbol;Acc:24636] |
Retrocopy-Parental alignment summary:
>retro_amel_253
AATTCCCAGGTCAAGAGAGAGGTCCAGCCGCCTGTCCATCCCATGCCACTAAATCCAGATGCCAGAGCCTCCAGCCTCTC
TGAAATTTCTCCTCCCAAAGCACTGAAGATGTTTCAGGCACCTGCAAGAGAGACTTGTGTGCTAAGTCAGAAGACAGTCT
GCCCAATGGAGTGTGTCTGGGCCTCTAGCAGGTGGTTCACAGGAGCTGCTTCCGTTGCTCCTAATGCAACAACAGACTTA
GTCTAGGAGCATACGCGTCTTTCATGGGAGAATCTACCGCAAGCCTCACTTCAACCAACTCTTCAAAGCTAAAGGTAACT
ATGATGAAGGCTTTGGGCACAGACCACACAAGGATCTGCAGGCAAGCAAAACTGAAAATGAAGGGACTTTGGAGAGACCA
GCCCAGCTTCCAAATGCAAGGGAGACCCCTCAGAGCCCAGGACTAGAAGATGTCCCCATTGCTAAGGTGGGTGTGCTGAC
AGCAGGTATGGAAGCCAAGGCCTCCTCTCAGCCAGAGAAAGAGGACAAGCCAGCTGAAACAAAGAAGCTGAAGATCACCT
GGCCGCCGCCCCCCTGCCCCCCAGAACTTGGTAGTTCCACAAGTACCTTGGAGGAAGGGATCCAAGTATCCAAGCCCAAA
CGGCCTCCTGAGGATGAAAGCAGCAAGCCTGAAGCTCCCGAGGACGTAGAGCTGGATCTGAAGAAGCTAAGATGATCTCC
TTCGCTGAAAGAAAGAAGCCACCCATTCACTGTAGCAGCTTCATTTCGAACCACTTCAGTCAAGAGCCCCAAAAATCTTG
CCCCCATCCATAAGGAAAGGCTGGAGCATGTCAGAGCAGAGTAAGGAGTTTACAGGAGGAATGCCAGCAGGAAGCAAACA
AGCAGAAACTGCCATTACCTCCAAAAAGAATGGTAGTGTGGGGAAAACAACCTGGCAAAACCAGGAATCCGGAGGAGGGG
AGACAGGGAGAAGGAAGGGAGTTGGTGCTTTCGAGATGGGGAGTGAGAATCTTCTAGGAAATGGTGCAAACTTAGATGAA
GATGACAGAAACCTCAAACAGCACCCTCCACTAGCACCCAAGCCTACAAACTGGTCCAGCTTTGCAGAGAATACCTCCCC
TAAAGAATTCACCACCCAGAATCAGAAATCCCAGGATGGGGGGTTCTGGGAGGGAGAAGTAGTCAAAGAGCTGTGTGTGG
AGAAACAGAGAAGTCAGTACTATGATGAGGATGAGGATGAGGAA
ORF - retro_amel_253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.78 % |
| Parental protein coverage: | 54.02 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | NSQVKSEVQQPVHPKPLNPDARASSLSESSPPKAVKKFQAPARETCVECQKTVYPMERLLANQ-QVFHVS |
| NSQVK.EVQ.PVHP.PLNPDARASSLSE.SPPKA.K.FQAPARETCV..QKTV.PME...A...QV.H.S | |
| Retrocopy | NSQVKREVQPPVHPMPLNPDARASSLSEISPPKALKMFQAPARETCVLSQKTVCPMECVWASS<QVVHRS |
| Parental | CFRCSYCNNKLTNSLGTYASL-HGRIYCKPHFNQLFKAKGNYDEGFGHRPHKDLWASKNENEGILERRAQ |
| CFRCS.CNN.L..SLG.YAS..HGRIY.KPHFNQLFKAKGNYDEGFGHRPHKDL.ASK.ENEG.LER.AQ | |
| Retrocopy | CFRCS*CNNRL--SLGAYASF<HGRIYRKPHFNQLFKAKGNYDEGFGHRPHKDLQASKTENEGTLERPAQ |
| Parental | LPNAGETPQSPGVEDAPIAKVGVLTASMEAKASSQPEKEDKPAETKKLKIAWPP---PTELSSSGSILEE |
| LPNA.ETPQSPG.ED.PIAKVGVLTA.MEAKASSQPEKEDKPAETKKLKI.WPP.....EL.SS.S.LEE | |
| Retrocopy | LPNARETPQSPGLEDVPIAKVGVLTAGMEAKASSQPEKEDKPAETKKLKITWPPXXXXXELGSSTSTLEE |
| Parental | GIKVSKPKWPPEDEISKAEAPEDIDLDLKKLRRSSSLKERSRPFTVAASFRTTSVKS-PKISSPPIRRGW |
| GI.VSKPK.PPEDE.SK.EAPED..LDLKKLR.S.SLKERS.PFTVAASFRTTSVKS.PKI..P.IR.GW | |
| Retrocopy | GIQVSKPKRPPEDESSKPEAPEDVELDLKKLR*SPSLKERSHPFTVAASFRTTSVKS>PKILPPSIRKGW |
| Parental | STSEQSEEFTGGMTAERKEVENANTFEKNGGVGKTTWQNQESGGGETGRRSKEDHGFEMGSENLTENGAN |
| S.SEQS.EFTGGM.A..K..E.A.T..KNG.VGKTTWQNQESGGGETGRR.K....FEMGSENL..NGAN | |
| Retrocopy | SMSEQSKEFTGGMPAGSKQAETAITSKKNGSVGKTTWQNQESGGGETGRR-KGVGAFEMGSENLLGNGAN |
| Parental | LDEDDRNLNQPSPLEPKPTNWSSFADSTSPEEFTTQNQKSQDVGFWEGEVVQELSVEEQIKRNRYYEEEE |
| LDEDDRNL.Q..PL.PKPTNWSSFA..TSP.EFTTQNQKSQD.GFWEGEVV.EL.VE.Q..R..YY.E.E | |
| Retrocopy | LDEDDRNLKQHPPLAPKPTNWSSFAENTSPKEFTTQNQKSQDGGFWEGEVVKELCVEKQ--RSQYYDEDE |
| Parental | EDE |
| ..E | |
| Retrocopy | DEE |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ailuropoda melanoleuca was not studied using RNA-Seq expression data.
Ailuropoda melanoleuca was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_amel_253 retrocopy.
Ailuropoda melanoleuca was not studied using FANTOM5 data.
retro_amel_253 was not experimentally validated.
Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000001243 | 1 retrocopy |
retro_amel_253 ,
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