RetrogeneDB ID: retro_shar_828

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867610.1:290233..291233(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTEN
• Ensembl ID: ENSSHAG00000003709
• Aliases: None
• Description: phosphatase and tensin homolog [Source:HGNC Symbol;Acc:9588]

Sequence

>retro_shar_828
TATACAATCTATGTGCTGAAACATTATGATGCCACTAAATTTAACAGTAGAGTTGCACAGTATCCTTTTAAAGACAACTC
ATCCCAGCTAGAGCTCATCAAACACTTTTGTAAGGATCTTGACCTGTAGCTAAGTGAAGATGACAATAATGTTGTTGCAA
TTCACTGCAAAGTAGAAAAGGGACGAACTGATGTAATGATTTATGCATATTTATTACATCGAGGAAAGTTTTTAAAGGCA
CAAGAGGCTCTAGATTTCTATGGGGAAGTCAGAACCAGAGACAAAATAGGAGTAACTATTCCCAGCCAGAGGCACTATAT
GTATTACTATAGCCACCTGTTAAAGCACCATTTGGATTATAGACCAATGGCCTAACTCTTTCACAAGATGATATTTGAAA
CAATTCCATGTTCAGTGATGGAACTTGCAATCCTCAATTTGTAGTATACCAGCTGAAAGTGAAGATCTATACATCCCCTT
TAGGGCCTACAAGGCAGAAAGATAAAGTACATGTATTTTGAATTCCCCGTGCCTTTGATGGTATACAGTGACATTAAAGT
GGAATTCTTCCACAAGCAGAACAAGATGCTCAAAAAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAG
AACCAGAGGAAAACTCGAAGTAGAAAATGGAAGTCTTTGTGGAGATCAAGAGATCAATAGTGGCAGAATCTAGTGATCAG
ATAATGACAAAGAAGGTCTCATACTCACATTATCCAAAAATAATCATGAAAAAGCTAATAAAGACAAGGCCAACAGATAC
TTTTCTCCAAACTTTAATGTGAAGCTTTTCTTCACAAAAACTGTAATGGAGCCAGCAAACACAGGAGCCTGTGTTCCATT
TAGGATACCCCGGACATTAGTGACAATGAACTTAATCATCATAGATACTTGAAAACCACTAACTCTGATCCAGAGAACAA
GCCTTTTGATGAAGATCAACACGCACAGATCCCAAAAGTC

Alignment

ORF - retro_shar_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YNLCAERHYDATKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICA
          Y......HYDATKFN.RVAQYPF.D.N..QLELIK.FC.DLD..LSEDDN.V.AIHCK..KGRT.VMI.A
Retrocopy YTIYVLKHYDATKFNSRVAQYPFKD-NSSQLELIKHFCKDLDL*LSEDDNNVVAIHCKVEKGRTDVMIYA

Parental  YLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSHLLKHHLDYRPVALLFHKMMFETIP-MF
          YLLHRGKFLKAQEALDFYGEVRTRDK.GVTIPSQR.Y.YYYSHLLKHHLDYRP.A.LFHKM.FETIP.MF
Retrocopy YLLHRGKFLKAQEALDFYGEVRTRDKIGVTIPSQRHYMYYYSHLLKHHLDYRPMA*LFHKMIFETIP<MF

Parental  SGGTCNPQFVVCQLKVKIYTSPSGPTRREDK-YMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWV
          S.GTCNPQFVV.QLKVKIYTSP.GPTR..DK.YMYFEFP.PL.V..DIKVEFFHKQNKMLKKDKMFHFWV
Retrocopy SDGTCNPQFVVYQLKVKIYTSPLGPTRQKDK>YMYFEFPVPLMVYSDIKVEFFHKQNKMLKKDKMFHFWV

Parental  NTFFIPGPEENSDK-VENGSLCGDQEIDSIGSAERSDNDKEYLILTLSKNDLDKANKDKANRYFSPNFKV
          NTFFIP.P.E...K.VENGSLCGDQEI.S.G....SDNDKE.LILTLSKN...KANKDKANRYFSPNF.V
Retrocopy NTFFIPEP-EENSK<VENGSLCGDQEINS-GRI**SDNDKEGLILTLSKNNHEKANKDKANRYFSPNFNV

Parental  KLFFTKTVEEPANPEASSSTSV-TPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
          KLFFTKTV.EPAN..A.......TPD.SDNE..H.RY..TT.SDPEN.PFDEDQH.QI.KV
Retrocopy KLFFTKTVMEPANTGACVPFRI<TPDISDNELNHHRYLKTTNSDPENKPFDEDQHAQIPKV

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_828 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009252	1 retrocopy	retro_chof_578,
Homo sapiens	ENSG00000171862	1 retrocopy	retro_hsap_4245,
Gorilla gorilla	ENSGGOG00000000893	1 retrocopy	retro_ggor_2846,
Nomascus leucogenys	ENSNLEG00000012141	1 retrocopy	retro_nleu_1280,
Pongo abelii	ENSPPYG00000002448	1 retrocopy	retro_pabe_3393,
Sarcophilus harrisii	ENSSHAG00000003709	1 retrocopy	retro_shar_828 ,
Sus scrofa	ENSSSCG00000010440	2 retrocopies	retro_sscr_236, retro_sscr_237,