RetrogeneDB ID: | retro_ocun_504 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 12:50615989..50616732(+) | ||
| Located in intron of: | ENSOCUG00000015539 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TATDN3 | ||
| Ensembl ID: | ENSOCUG00000004792 | ||
| Aliases: | None | ||
| Description: | TatD DNase domain containing 3 [Source:HGNC Symbol;Acc:27010] |
Retrocopy-Parental alignment summary:
>retro_ocun_504
GATGTGTTGGAGGAAGCCAAGAAGGGCAACGTTATGGCCCTTATGGCAGTTGCTGAACATTCAGGAGAATTTGAAAAGAT
TATGCAACTTTCAGAAAGGTATAATGGGCTTGTCCTGCCATGTTTGGGTGTTCACCCAGTCCAAGAACTACCATCAGAAG
ATCAGAGGAGTGTCACATCGAAGGATTTGGAAGTGGCTTTGCCTATTATTGGGCATTATAAGGATCAGTTATTGGCAATT
GGAGAAGTTGGACTAGATTTCACCCCCAGATTTGCTGGCACTGATGAACAGAAGGAAGAGCAAAGACAAGTCCTAATCAA
ACAAGTCCAATTAGCCAAAAGACTAAATTTGCCTTTAAATGTTCATTCCCGTTCAGCTGGAAGACCTTCCATCAACCTCT
TACATGAGCAAGGTGCTGTCAAAGTACTGCTGCACGGATCTGATGATCGGCCATCTGTAGCCATGAAGGAGTAAGAGCTG
GGTACTTCTTCTCCATACCCACTTCTGTCGTAAATGGACAGAAGCAGAAACTTGTAAAACAGTTGCCTTTATCTTCTATA
TGCTTAGAAACAGATTTGCCTGCACTAGGACCAGTACAACAAGTGCGAAATGAGCTCAGGAACATTTCCATTTCAGCAGA
ACATATTGTCTAAGTGAAAGGGATCTCAGTGGAAGAAGTTATAGAAGTGACAACACAGAACACATTGGAATGGTTTCCCA
AGCGTCAACACCTGCTGCAGAAA
ORF - retro_ocun_504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.0 % |
| Parental protein coverage: | 90.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DVLEEAKKVNVMALVAVAEHSREFEKIMQLSERYNGFVLPCLGVHPVQELPSEDQRSVTLKDLEVALPII |
| DVLEEAKK.NVMAL.AVAEHS.EFEKIMQLSERYNG.VLPCLGVHPVQELPSEDQRSVT.KDLEVALPII | |
| Retrocopy | DVLEEAKKGNVMALMAVAEHSGEFEKIMQLSERYNGLVLPCLGVHPVQELPSEDQRSVTSKDLEVALPII |
| Parental | ERYKDRLLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRPTVSLLREQGAD |
| ..YKD.LLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRP...LL.EQGA. | |
| Retrocopy | GHYKDQLLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRPSINLLHEQGAV |
| Parental | KVLLHAFDGRPSVAM-EGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPVKQVRNEPRN |
| KVLLH..D.RPSVAM.EGVRAGYFFSIP.S....GQKQKLVKQLPL.SICLETD.PALGPV.QVRNE.RN | |
| Retrocopy | KVLLHGSDDRPSVAM<EGVRAGYFFSIPTSVV-NGQKQKLVKQLPLSSICLETDLPALGPVQQVRNELRN |
| Parental | ISISAEYIAQVKGISVEEVIEVTTQNAMKLFPKLQHLLKK |
| ISISAE.I..VKGISVEEVIEVTTQN....FPK.QHLL.K | |
| Retrocopy | ISISAEHIV*VKGISVEEVIEVTTQNTLEWFPKRQHLLQK |
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 | 6 .79 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .91 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .94 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_504 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_504 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_504 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 | ENSOCUG00000004792 | 1 retrocopy |
retro_ocun_504 ,
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