RetrogeneDB ID: | retro_shar_701 | ||
Retrocopy location | Organism: | Tasmanian devil (Sarcophilus harrisii) | |
| Coordinates: | GL857630.1:22871..23669(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSHAG00000002078 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C20orf96 | ||
| Ensembl ID: | ENSSHAG00000002453 | ||
| Aliases: | None | ||
| Description: | chromosome 20 open reading frame 96 [Source:HGNC Symbol;Acc:16227] |
Retrocopy-Parental alignment summary:
>retro_shar_701
ACCCAAATGTTCAGAGAAATGATTAAGTTCAGGAAGGACTCACTAGACAAACTTAAACAACATGTTGCCTCTCTTACTGT
CAGCAACCAAGGAGCTGGCAAAAAAAGATCCAGAACATAGAAGCCATGACTGTAGAGAAAGTGCAGAAGCTTCTTTGGCA
GCAAGATATGTTTGGGACTGTCATTAACACTCCAGATATGCAAACCATAGACAAATGCAAAACATGAAGAGCAAGCTAGA
GAAGTGGGAAGCAGAGATAACGGTCAGAGTGAATGAACTGGAGCAGCAGTTGAAAAAGTTGAAAGTTAAAATTAATAATA
CCCAAGAGGAGCTGAATTTCCTGAGTACCTATATGAATATTAATACCCAATTAAGTCTATGCAGATTGCCGACCTCATGT
GCCAGATCCAGGATGTGAAAGATAGCAGTCAGGATGAACTAGATGAGTTGGAGGAGATACTCAAGAATGTGCTTCAAACA
TTGTCAAAGAAGCTGATGATGAAGTCAGAGAAAGTCTTAAATGATATGGCCAAGAGAACCATCCTTCCCTATCAAATTGG
TCTTATGAAGAAGACCTTAAGCAACCAGCTACTATTGGAACAGATGGTTCAGTTCAGAGTGCACATTGATCATATGAAGA
AGGAACTTTCCAATCTGAAGACTCAGGTGAAAGATCTCCAGATGAAGAGAAAAGACCCAAGAGAGATGATCTTTGCCAGT
GTCCTGCTTTGGAAACCCAAGTATACTCCAGACACGGATTTCATCCTCATTATCCCCCCAGAAGAAATTCTTTCCTTT
ORF - retro_shar_701 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.3 % |
| Parental protein coverage: | 98.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | TQILKEIVKFRKDSLAELKQNVDSLTVSNQ-ELAKK-IQDVEAFTAEKVRKLLRQQDVFGTLISTLE-YA |
| TQ...E..KFRKDSL..LKQ.V.SLTVSNQ.ELAKK.IQ..EA.T.EKV.KLL.QQD.FGT.I.T...YA | |
| Retrocopy | TQMFREMIKFRKDSLDKLKQHVASLTVSNQ>ELAKK>IQNIEAMTVEKVQKLLWQQDMFGTVINTPD<YA |
| Parental | NHIQMQDMKSKLEKWEAETKVRVNDLEQQLTKLKRKINNAQEELNFLSTYM-DHEYPIKSLEIANLVRQV |
| NH.QMQ.MKSKLEKWEAE..VRVN.LEQQL.KLK.KINN.QEELNFLSTYM....YPIKS..IA.L..Q. | |
| Retrocopy | NHRQMQNMKSKLEKWEAEITVRVNELEQQLKKLKVKINNTQEELNFLSTYM<EY*YPIKSMQIADLMCQI |
| Parental | QGVKDSSQNELDELEEIRKNVLQTLSKKLMVKSEKVLNIMAKRTILPYQTALMKRTLSNQLLLKQMVQFR |
| Q.VKDSSQ.ELDELEEI.KNVLQTLSKKLM.KSEKVLN.MAKRTILPYQ..LMK.TLSNQLLL.QMVQFR | |
| Retrocopy | QDVKDSSQDELDELEEILKNVLQTLSKKLMMKSEKVLNDMAKRTILPYQIGLMKKTLSNQLLLEQMVQFR |
| Parental | VHIDRMKKELPKLKAQVKDLQMKRQDPREVIFANILLRKPKCTPDMDVILNIPPEEILPF |
| VHID.MKKEL..LK.QVKDLQMKR.DPRE.IFA..LL.KPK.TPD.D.IL.IPPEEIL.F | |
| Retrocopy | VHIDHMKKELSNLKTQVKDLQMKRKDPREMIFASVLLWKPKYTPDTDFILIIPPEEILSF |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Sarcophilus harrisii was not studied using RNA-Seq expression data.
Sarcophilus harrisii was not studied using ChIP-Seq data.
Sarcophilus harrisii was not studied using EST data.
Sarcophilus harrisii was not studied using FANTOM5 data.
retro_shar_701 was not experimentally validated.
Retrocopy orthology:
Sarcophilus harrisii 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 | |
|---|---|---|---|
| Sarcophilus harrisii | ENSSHAG00000002453 | 1 retrocopy |
retro_shar_701 ,
|