RetrogeneDB ID: retro_shar_151

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834474.1:1136635..1137517(-)
• Located in intron of: ENSSHAG00000012819

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009835
• Aliases: None
• Description: None

Sequence

>retro_shar_151
CCTGTGATTGAAGAGCTTGACTCTTGAGGTCAAAAAAGGAGAAGATATACTCCTTTTGATCTGAAAAAAAATGAAGGATT
TGAAAAAGGATTGCATTCTTTATGGGGCTACATCATCTTATGTTAAGATGTTACTAAAGAATTTGGATTATGAAATCTTA
AACCCCAGTGATTGGAAACCTATAGCAAGGACATGTTTAGAACCTGGACAAAACTTGTTGTGGCTTTCAAAGTATCATGA
ACTTTGCAGGATACAAGCCCAACATAATAAGGAAACTGGAGTTATTATACAAATCACCTTTGACCAATTAGCAGGTGAAG
GTCAGCATGCAGATGCTATAGCACAGATTAATTGCCCCATTAATTAATGTGCTTATACCCCATATGAGCAAATTGCTCCT
GCTACAATCAAAGCTTAGTGTTCTCTCCCAGAAAAAGATGGAGGGGAAGTCTTCACAAAAATAGATCAAAGTCCCAATGA
ACCTTTTGATGATTTTGTGGGATGTTTGCAAACAGCTGTCACAAGAACCATTAGAGAAAATGCAGCTACAAGAATTATGA
TAAGACAACTGGCTAAGGAAAATGCTAATGAGGTTTGCAGAAGAATTATATGGGGACTACACAAAATACTCCTTTAAAGG
AGATCATAAGATGCTATGCTACAGTGGGCACAGATGCTTATTATACCCAGACTATGATGAACATGGGAAGACAGAGTCCC
TTTTGGCAAGGGACTTCTAGAGAAACTCATTGTTGCTTTCAATGTGGAAAAGTTGGACATCTGAGAGCTCAATGTAGGCA
AAAACATAGAGTGAGAGGACAGGGTGAGAGAAGACCTAAAATTTTATGTCCAAAATGCCACAAGGGCTTCCACTGGGCCT
CA

Alignment

ORF - retro_shar_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.45 %
• Parental protein coverage: 87.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVVEKLNSSGQERRRYTPFNLEII-KDLKKACILYEATSSYVKMLLQNLAYEILTPSDWKSIARTCLGPG
          PV.E.L.S.GQ.RRRYTPF.L....KDLKK.CILY.ATSSYVKMLL.NL.YEIL.PSDWK.IARTCL.PG
Retrocopy PVIEELDS*GQKRRRYTPFDLXXX>KDLKKDCILYGATSSYVKMLLKNLDYEILNPSDWKPIARTCLEPG

Parental  QNLLWLSEHSELCRIQIQQNKQTGVNTPITYDQLTGVSSY----ADISAQIN-YPIAAFQEIASAAIEAW
          QNLLWLS...ELCRIQ.Q.NK.TGV...IT.DQL.G........A.I...IN.........IA.A.I.A.
Retrocopy QNLLWLSKYHELCRIQAQHNKETGVIIQITFDQLAGEGQHADAIAQINCPIN*CAYTPYEQIAPATIKA*

Parental  GFLPGNKTDEKPSKIEQGPNEPFADFVGPLQTA----IGENAAKEIMIRQLAKENANEVCRRIILGLCK-
          ..LP.....E...KI.Q.PNEPF.DFVG.LQTA....I.ENAA..IMIRQLAKENANEVCRRII.GL.K.
Retrocopy CSLPEKDGGEVFTKIDQSPNEPFDDFVGCLQTAVTRTIRENAATRIMIRQLAKENANEVCRRIIWGLHK<

Parental  DAPLEEIIRRCATVGTNTFYAQAMMQTSQDPN--QGTSRETRQCFQCGKVGHLKGQCWHKDRAQQSGDNH
          ..PL.EIIR..ATVGT...Y.Q.MM.........QGTSRET..CFQCGKVGHL..QC..K.R....G...
Retrocopy NTPLKEIIRCYATVGTDAYYTQTMMNMGRQSPFWQGTSRETHCCFQCGKVGHLRAQCRQKHRVRGQGERR

Parental  PDSDSKQQNPGIFWTA
          P.........G..W..
Retrocopy PKILCPKCHKGFHWAS

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_151 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009835	3 retrocopies	retro_shar_151 , retro_shar_195, retro_shar_429,
Sarcophilus harrisii	ENSSHAG00000016712	2 retrocopies	retro_shar_169, retro_shar_562,