RetrogeneDB ID: | retro_ocun_1903 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | X:82014896..82016031(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000023356 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GALT | ||
| Ensembl ID: | ENSOCUG00000024714 | ||
| Aliases: | None | ||
| Description: | galactose-1-phosphate uridylyltransferase [Source:HGNC Symbol;Acc:4135] |
Retrocopy-Parental alignment summary:
>retro_ocun_1903
ATGTCGCGCGGCGGAACCGACTCCGAGCAGCGCCAGCAGGCGTCAGAGGCAGACGCCACCAAAACAGCCTTCCTGGCAAG
CGAGCATCAGCATATCCGCTACAACCCGCTGCAGGATGAGTGGGTGCTGGTGTCAGCTCACCGCATGAAGCGGCCCTGGC
AGGGGCAAGTGGAGCCCGAGCCTCTGAAGACAGTGCCCCGCCACGACCCCCTCAACCCTCTGTGTCCCGGGGCCACCCGG
GCCAATGGAGAGGTGAATCCTAACTATGATGGCACCTTCCTGTTCGACAACGACTTCCCAGCTCTGCAGCCTGATGCCCC
TAATCCAGGACCCAGCGATCACCCGCTTTTCCAAGTGCAGGCTGCCCGAGGAGTTTGTAAGGTCATGTGCTTCCACCCCT
GGTCGGATGTGACGCTGCCACTCAATGTCAGTCCCTGAGATCCGGGCTGTCGTCGATGCATGGGCCTCAGTCACAGAGGA
TCTGGGTGCTCAGTACCCTTGGGTGCAGATCTTTGAAAACAAAGGAGCCATGATGGGCTGTTCCAATCCCCACCCCCATT
GCCAGGTGTGGGCCAGCAGCTTCCTGCCAGATATTGCCCAGCGCGAGGAGAGATCTCAGCGGGCCTATCACAGTCAACAC
GGAGAGCCTCTGCTGATGGAGTATGGCCGCCAGGAGCTGCTCCGGAAGGACCATCTGGTCCTAACCAGCGAGCACTGGTT
GGTGCTGGTCCCCTTCTGGGCAGTGTGGACCTTGCAGACACTGCTGCTGCCCCGTCGCCATGTGTGGTGGCTGCCTGAGC
TGACCCCCACTGAGCGCGATGATCTGGCCTCCATCATGAAGAAGCTCTTGACCAAGTACGACAACCTGTTTGAGACTTCC
CTTCCCTACTCCATGGGCTGGCATGGAGCTCCCACAGGGTCAGAGGCTGGGGCCACCTGGGACCACTGGCAGCTGCACGC
TCACTACTACCCTCCACTCCTCCGCTCTGCCACTCACCGCAAATTCATGGTTGGCTATGAAATGCTTACTCAGGCTCAGA
GGGACCTCACTCCTGAGCAGGCTACAGAGAGACTAAGGGCACTTCCTGAGGTTCATTACCGCCTGAGGCAGAAGGACAAG
GAGACTGCGGCCATC
ORF - retro_ocun_1903 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.04 % |
| Parental protein coverage: | 99.74 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSRGGTDSEQRQQASEADATKTAFRASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP |
| MSRGGTDSEQRQQASEADATKTAF.ASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP | |
| Retrocopy | MSRGGTDSEQRQQASEADATKTAFLASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP |
| Parental | LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQAQAARGVCKVMCFHPWSDVTLP |
| LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQ.QAARGVCKVMCFHPWSDVTLP | |
| Retrocopy | LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQVQAARGVCKVMCFHPWSDVTLP |
| Parental | L-MSVPEIRAVVDAWASVTEDLGTQYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY |
| L.MSVPEIRAVVDAWASVTEDLG.QYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY | |
| Retrocopy | L>MSVPEIRAVVDAWASVTEDLGAQYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY |
| Parental | HSQHGEPLLMEYGRQELLRKDRLVLTSEHWLVLVPFWAVWPFQTLLLPRRHVRRLPELTPTERDDLASIM |
| HSQHGEPLLMEYGRQELLRKD.LVLTSEHWLVLVPFWAVW..QTLLLPRRHV..LPELTPTERDDLASIM | |
| Retrocopy | HSQHGEPLLMEYGRQELLRKDHLVLTSEHWLVLVPFWAVWTLQTLLLPRRHVWWLPELTPTERDDLASIM |
| Parental | KKLLTKYDNLFETSFPYSMGWHGAPTGSEAGAAWDHWQLHAHYYPPLLRSATVRKFMVGYEMLAQAQRDL |
| KKLLTKYDNLFETS.PYSMGWHGAPTGSEAGA.WDHWQLHAHYYPPLLRSAT.RKFMVGYEML.QAQRDL | |
| Retrocopy | KKLLTKYDNLFETSLPYSMGWHGAPTGSEAGATWDHWQLHAHYYPPLLRSATHRKFMVGYEMLTQAQRDL |
| Parental | TPEQAAERLRALPEVHYRLRQKDKETAAV |
| TPEQA.ERLRALPEVHYRLRQKDKETAA. | |
| Retrocopy | TPEQATERLRALPEVHYRLRQKDKETAAI |
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 .00 RPM | 17 .99 RPM |
| SRP017611_kidney | 0 .10 RPM | 23 .41 RPM |
| SRP017611_liver | 0 .00 RPM | 15 .65 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1903 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1903 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1903 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000024714 | 1 retrocopy |
retro_ocun_1903 ,
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