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 symbol: C20orf96
• Ensembl ID: ENSSHAG00000002453
• Aliases: None
• Description: chromosome 20 open reading frame 96 [Source:HGNC Symbol;Acc:16227]

Sequence

>retro_shar_701
ACCCAAATGTTCAGAGAAATGATTAAGTTCAGGAAGGACTCACTAGACAAACTTAAACAACATGTTGCCTCTCTTACTGT
CAGCAACCAAGGAGCTGGCAAAAAAAGATCCAGAACATAGAAGCCATGACTGTAGAGAAAGTGCAGAAGCTTCTTTGGCA
GCAAGATATGTTTGGGACTGTCATTAACACTCCAGATATGCAAACCATAGACAAATGCAAAACATGAAGAGCAAGCTAGA
GAAGTGGGAAGCAGAGATAACGGTCAGAGTGAATGAACTGGAGCAGCAGTTGAAAAAGTTGAAAGTTAAAATTAATAATA
CCCAAGAGGAGCTGAATTTCCTGAGTACCTATATGAATATTAATACCCAATTAAGTCTATGCAGATTGCCGACCTCATGT
GCCAGATCCAGGATGTGAAAGATAGCAGTCAGGATGAACTAGATGAGTTGGAGGAGATACTCAAGAATGTGCTTCAAACA
TTGTCAAAGAAGCTGATGATGAAGTCAGAGAAAGTCTTAAATGATATGGCCAAGAGAACCATCCTTCCCTATCAAATTGG
TCTTATGAAGAAGACCTTAAGCAACCAGCTACTATTGGAACAGATGGTTCAGTTCAGAGTGCACATTGATCATATGAAGA
AGGAACTTTCCAATCTGAAGACTCAGGTGAAAGATCTCCAGATGAAGAGAAAAGACCCAAGAGAGATGATCTTTGCCAGT
GTCCTGCTTTGGAAACCCAAGTATACTCCAGACACGGATTTCATCCTCATTATCCCCCCAGAAGAAATTCTTTCCTTT

Alignment

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_701 was not experimentally validated.

Homology

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.

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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 ,