RetrogeneDB ID: | retro_ocun_205 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 1:55082578..55083442(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000002637 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM122C | ||
| Ensembl ID: | ENSOCUG00000029737 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 122C [Source:HGNC Symbol;Acc:25202] |
Retrocopy-Parental alignment summary:
>retro_ocun_205
ATGGCTCAGGAGAAGATGGAGCTGGACCTAGAGCTGCCTCCGGGTACGGGCGGGAGCCCGGCGGAGGGCGGCGGCAGTGG
CGGCGGCGGGGGCCTTAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCGAGCGCCAGGCGGAACAGCACGACGTTCCCGAGCCGCCACGGCCTGCTGCTGCCGGCCTCCCCCGTCCGCATG
CACAGCAGCCGCTTGCACCAAATCAAACAGGAGGAGGGCATGGACTTGATCAACCGAGAGACGGTCCACGAGCGCGAGGT
GCAGACCGCAATGCAGATCAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCC
CGAAGCGCATCGATTTCATTCCGGTGTCCCCAGCACCGTCACCCACCCGGGGGATTGGGAAGCAGTGTTTCTCACCATCC
TTGCAAAGTTTTGTGAGTAGCAACGGATTGCCCCCGAGCCCTATCCCCAGCCCAACGACCCGATTTACTACTCGGAGAAG
CCAGAGTCCCATCAACTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAGTATCAGC
CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCCGACGTTGCACAGCTGTCAGATCCCGGGGTGTGTGTGTCT
TCGGATACCCTTGACGGAAACAGCAGCAGTGCGGGATCTTCCTGCAACTCACCAGCGAAAGCCAGCACTGCCGCCGACTC
TCCCGTGTCACCTGCCCAGGCAGCCTCGCCGTTCATCCCTGTAGATGAGCTTGCATCTAAGTGA
ORF - retro_ocun_205 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.16 % |
| Parental protein coverage: | 73.36 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LRRSSSAPMINGLGDNSQVFQDEAIRIRRNSSTFMSQQCLLFPPPSISTSLSRVHQIKQEESMDLIDRET |
| LRRS.SAP.I.GL.D.S.VFQ.EA...RRNS.TF.S...LL.P........SR.HQIKQEE.MDLI.RET | |
| Retrocopy | LRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPSRHGLLLPASPVRMHSSRLHQIKQEEGMDLINRET |
| Parental | LHEQEVQTAIQISQSWEKCLNLNDNDLEKPLSLKCIDLISVLPVVSPSQGIEKQCFSPSLRTSVSCAGFP |
| .HE.EVQTA.QIS.SWE....L.DND.EK..S.K.ID.I.V.P..SP..GI.KQCFSPSL...VS..G.P | |
| Retrocopy | VHEREVQTAMQISHSWEESFSLSDNDVEKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQSFVSSNGLP |
| Parental | PSPSPSPSQQ-NAISSHNPTNIVRPSILGPIKRKGELTLEEPPKKIFI-VTSNIPSDISQLSE |
| PSP.PSP........S..P.N..RPS.LGP.KRK.E...E..PK..F...T....SD..QLS. | |
| Retrocopy | PSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLSD |
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 |
|---|---|---|
| SRP017611_brain | 15 .78 RPM | 0 .00 RPM |
| SRP017611_kidney | 11 .96 RPM | 0 .10 RPM |
| SRP017611_liver | 4 .08 RPM | 0 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_205 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_205 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_205 has 6 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_35 |
| Mus musculus | retro_mmus_22 |
| Rattus norvegicus | retro_rnor_651 |
| Bos taurus | retro_btau_103 |
| Canis familiaris | retro_cfam_181 |
| Equus caballus | retro_ecab_91 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000156500 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000002084 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000029737 | 1 retrocopy |
retro_ocun_205 ,
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