RetrogeneDB ID: | retro_ocun_1704 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018788:692120..692887(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM55A | ||
| Ensembl ID: | ENSOCUG00000000723 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 55A [Source:HGNC Symbol;Acc:25452] |
Retrocopy-Parental alignment summary:
>retro_ocun_1704
ATGGCTGTGGACAGGGTGGACGAAGGCTCACCATTGCTATCAGCATTGTATTCAGGGAATGTCACTCCCCCAGTCCCACC
ATATTTGCAAGAAAGCAGCCCCAGCACGGAACTCCCACCTCCATATATGGCTGTTGCTAATCCAGATGCAGCGGTATTCC
AGTAGTAAATTGCCGTACATGCCAGTCTCTCATCAATTTGGATGGCAAACTTCACCAGCCTGTGACTAAGGGCATGGTCT
GCAATGAAGCCACGCCAATCAAAAACCCACCATCAGGGAAGAAATATGTTAGATGCCCTTGTAATTGTCTCCTCATTTGT
AAGGACACATCTCGGCGAACAGGATGTCCAAGACCCAGCTGTAGACACATAATCACCCTTGGCCCAATAATGCTTACTTC
TGAACAGCCAGCTCAACCTGCTCTGCCAACCCAACAAGAAGGTCCAAGGGTTGTGTGTGGACACTGTGGAAGCACATTCC
TGTGGATGGAACTGAGGTTCAACACTCTGGCAAAATGCCCACACTGCAAAGCAATCTCCTCCGTGGACAGTGCACTTCCA
CGAAGACCCTGCTGTGCATACATTAGTGTTGGAATGATATGTATTTTCACTGGAGTTGGGTTAACTGTTGGCACCCAACA
CTTGGCTAGGCGATTTCGTGCAACCTATGTTTCTTGGGCAACTGCTTATCTTTTAGGTCTGATCTGTCTTATCTGAGCTT
GTTATTGGGGAGTCATAAGACTCAGCTATCCAGAACACAGTTTTGCA
ORF - retro_ocun_1704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.5 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAADGVDERSPLLSASHSGNVTPTAPPYLQESSPRAELPPPYTAIASPDA-SGIPVINCRVCQSLINLDG |
| MA.D.VDE.SPLLSA..SGNVTP..PPYLQESSP..ELPPPY.A.A.PDA.SGIPV.NCR.CQSLINLDG | |
| Retrocopy | MAVDRVDEGSPLLSALYSGNVTPPVPPYLQESSPSTELPPPYMAVANPDA<SGIPVVNCRTCQSLINLDG |
| Parental | KLHQHVVKCTVCNEATPIKNPPSGKKYVRCPCNCLLICKDTSRRIGCPRPNCRRIITLGPVMLISEEQPA |
| KLHQ.V.K..VCNEATPIKNPPSGKKYVRCPCNCLLICKDTSRR.GCPRP.CR.IITLGP.ML.SE.QPA | |
| Retrocopy | KLHQPVTKGMVCNEATPIKNPPSGKKYVRCPCNCLLICKDTSRRTGCPRPSCRHIITLGPIMLTSE-QPA |
| Parental | QPALPIQPEGTRVVCGHCGNTFLWMELRFNTLAKCPHCKKISSVGSALPRRRCCAYITIGMICIFIGVGL |
| QPALP.Q.EG.RVVCGHCG.TFLWMELRFNTLAKCPHCK.ISSV.SALPRR.CCAYI..GMICIF.GVGL | |
| Retrocopy | QPALPTQQEGPRVVCGHCGSTFLWMELRFNTLAKCPHCKAISSVDSALPRRPCCAYISVGMICIFTGVGL |
| Parental | TVGTQDFARRFRATYVSWAIAYLLGLICLIRACYWGVIRVSYPEHSFA |
| TVGTQ..ARRFRATYVSWA.AYLLGLICLI.ACYWGVIR.SYPEHSFA | |
| Retrocopy | TVGTQHLARRFRATYVSWATAYLLGLICLI*ACYWGVIRLSYPEHSFA |
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 | 0 .17 RPM | 34 .05 RPM |
| SRP017611_kidney | 0 .20 RPM | 0 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .16 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1704 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1704 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1704 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000000723 | 2 retrocopies |
retro_ocun_1391, retro_ocun_1704 ,
|
| Oryctolagus cuniculus | ENSOCUG00000005025 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000003770 | 1 retrocopy |