RetrogeneDB ID: retro_shar_591

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850862.1:38025..39208(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000002654
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSSHAG00000007140
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_shar_591
ATGTTCTCTTGTGTTTCGAGTCTCAGGCCCAACCGCCCCTTCTTCCTTCGTCTTCCCTGCATCCCTGGTGTCTCTGAAGC
GGCTTCGGAGACTCGGGGACAGTGGTCTCTCCCCAGCCACGCCAGGACAGAATACAAAATCCAAAGATATTTTGGTACAA
GCAGTGTGGTCTACAGAAAGAAAAATAAGTCTTCTGTTCCTGTTGCAAAGTTTTCTGACAATATTCCAAAGAGCCAGAAT
GAAAAAAAATAAAAATGCAAATAACTTGTTGAATATTATAAAGAGTATGAAAGTTGAATTAGTTACATCAGACATGTTAG
AGGACAGAAAAACTCATACAACCAATAAACAAAGGAAGAAGGAGGTTAAAAACTTGGGGAGGACAAGTAGTGTAAGTCAG
AAAGCTGTGGAAGATTCTTCACCTGAGAGTCACCAGTCACTGAGTCCTGAATTAGTGGCTGCTGCAACTGCTGTTGCTGA
TTCTCTTCCTTTTAACAAACAATCAGTCAAATCAGAGTTGCTGAGTCAATTGAGGAAACATGAGACAGACTTCAAAGCAC
ACCAAGGAAAAGAAGCAATTAAAATAAATATCAGTGACATAATTTCAGATATGAAGATTGCCAAATCATCTGCCCCTCGA
ACTTATTCTAGACCAGACCATCAAATTCAGTTTGATGAAGAACATGGATTTTTGTCTGCGAAAGAATTGGGGGATCTTAA
TCCTAGGAAGAGGAAAGGATTATTCACAGGGAAGAGACTTAATGTTTTCCCTGTGCATGAAACAACACCTGAAGAGATAC
CTGAAACAGAAACATCACCGACACTTTGGGATGTGGAATTTGCTAAACAATTAGCCACAGTAAGTCAACAACTTCCCCAG
AATGCTTTTCAAGAGATAATCCAGTGGACAAAAGAAGGAAAACTTTGGACATTCCCAATTAACAATGAAGCTGGTATTGA
TGATGATGGTGGTGCTGATTTTCACGAACATATATTTTTGGACAAATACCTGGAAGGTTTTCCAAAACAAGGACCAATTC
GTCATTTCATGGAACTAGTTACTTGTGGACTCTCAAAAAACCCATTTCTAACTGTTAAAGAAAAAGTTGAGCATATAGAA
TGGTTTCAGAATTATTTCCATGAAAAAAAGAATATTCTTGAAGAAAATAACATTCAATTTGGC

Alignment

ORF - retro_shar_591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSRVSSLGPNRPLFLRLPCIPGGSEAATETRGQGALPGHARTEYKIQRYFGTSSVVYRKKNKSFVPVAK
          MFS.VSSL.PNRP.FLRLPCIPG.SEAA.ETRGQ..LP.HARTEYKIQRYFGTSSVVYRKKNKS.VPVAK
Retrocopy MFSCVSSLRPNRPFFLRLPCIPGVSEAASETRGQWSLPSHARTEYKIQRYFGTSSVVYRKKNKSSVPVAK

Parental  ISDNIPKSQNEKNKN-ANNLLNIIKSMKVELATSDVLEDRKTHTTNKQRKKEVKNLERTSSVSQKAVEDS
          .SDNIPKSQN......ANNLLNIIKSMKVEL.TSD.LEDRKTHTTNKQRKKEVKNL.RTSSVSQKAVEDS
Retrocopy FSDNIPKSQNXXXXX>ANNLLNIIKSMKVELVTSDMLEDRKTHTTNKQRKKEVKNLGRTSSVSQKAVEDS

Parental  SPESHQSLSPELVAAAAAVADSLPFKKQSVKSELLSQLRKHETDFKAHQGKEAIKISFSDIISDMKIAKS
          SPESHQSLSPELVAAA.AVADSLPF.KQSVKSELLSQLRKHETDFKAHQGKEAIKI..SDIISDMKIAKS
Retrocopy SPESHQSLSPELVAAATAVADSLPFNKQSVKSELLSQLRKHETDFKAHQGKEAIKINISDIISDMKIAKS

Parental  SAPRTYSRPDRQIQFDEEHGFLSAKELGDLNPRKSFRKGLFTGKRLNVFPVDETTPEEIPETETSPTLWD
          SAPRTYSRPD.QIQFDEEHGFLSAKELGDLNPRK..RKGLFTGKRLNVFPV.ETTPEEIPETETSPTLWD
Retrocopy SAPRTYSRPDHQIQFDEEHGFLSAKELGDLNPRK--RKGLFTGKRLNVFPVHETTPEEIPETETSPTLWD

Parental  VEFAKQLATISQQLPQNAFEEMIQWTKEGKLWTFPINNEAGIDDD-GADFHEHIFLDKYLEGFPKQGPIR
          VEFAKQLAT.SQQLPQNAF.E.IQWTKEGKLWTFPINNEAGIDDD.GADFHEHIFLDKYLEGFPKQGPIR
Retrocopy VEFAKQLATVSQQLPQNAFQEIIQWTKEGKLWTFPINNEAGIDDDGGADFHEHIFLDKYLEGFPKQGPIR

Parental  HFMELVTCGLSKNPFLTVKEKVEHIEWFRNYFHEKKNILEENNIQFG
          HFMELVTCGLSKNPFLTVKEKVEHIEWF.NYFHEKKNILEENNIQFG
Retrocopy HFMELVTCGLSKNPFLTVKEKVEHIEWFQNYFHEKKNILEENNIQFG

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_591 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591 ,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,