RetrogeneDB ID: retro_shar_129

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834422.1:939857..940631(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTRF1L
• Ensembl ID: ENSSHAG00000017997
• Aliases: None
• Description: mitochondrial translational release factor 1-like [Source:HGNC Symbol;Acc:21051]

Sequence

>retro_shar_129
GCCTTTCGATATCTATGGGCTGGTAGAACACTAGTCAGGGCCCCTAGTCATTCTGTGAGCTCTGGAAGCCTTCAGCTGGA
GGAACTCTTTGCCAACAGTGGGGCCATGAGAAGTTTCTTTGAATGCTTGGTGAAACCCAGGTTCCAGGCCCTGTCCCAGG
TCCAGGGACCGGAATTGGCAATAGTGGCCCAGAGATTGAGGAAGAAGGAACAGAAGCCTCAGGAGACAGAGCACCTGCTA
GAGGATGAGAATGAAGACATAAGGAAACTAATAGAAAGTGAAATAATATCCTATAAGAAAGAATTAATCAAATTGAAGCA
AAAGATAATCTTACTCTTGATTCCCTCAGAAGAAATACATGAAAATGACTTCATCTTGGAATTAACTGCTGGAGTTGGTG
GTCAAGAAGCTATGCTGTGTACTGCAGAGATGTTTGATATGTACCAGCAATATGCTACATATAAAAATGGCATTTGAATA
CTGGAATATTTTCCCAGTGAAATAGACGGCCCAAAACATGCATCTGCCAGTATTGGGGGACCAAAAGCTTATAGAAAAAT
GGAGTTTGAAGGAAGTGTGCATCGAGTACAACAAGTGCCAAAGACTGAAAAACAAGTCCATATGCACAACAGCATAATGA
CTACGGCAGTACTGTCCTAGCCTCCTGAAATTAGCCTGATAATCAATCCTAAAAGTTTATGAATTGAAACTAAGTGAGCT
AGTAGAGCTGGGAACACTACTGACAGTGCTGTTCGAATAACCCATCTTCCAACA

Alignment

ORF - retro_shar_129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 68.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVRCLWAGGALVRAPSRPVSSGNLQLEELFASGGAMRSFLERLEKPRFQAPSWVQGPELAMATQRLREKE
          A.R.LWAG..LVRAPS..VSSG.LQLEELFA..GAMRSF.E.L.KPRFQA.S.VQGPELA...QRLR.KE
Retrocopy AFRYLWAGRTLVRAPSHSVSSGSLQLEELFANSGAMRSFFECLVKPRFQALSQVQGPELAIVAQRLRKKE

Parental  RELQETEQLLEDENEDIRKLAENEIISCQKELTKLKQKIILLLIPSEETDENDLILELTAGVGGQEAMLF
          ...QETE.LLEDENEDIRKL.E.EIIS..KEL.KLKQKIILLLIPSEE..END.ILELTAGVGGQEAML.
Retrocopy QKPQETEHLLEDENEDIRKLIESEIISYKKELIKLKQKIILLLIPSEEIHENDFILELTAGVGGQEAMLC

Parental  TSEMFDMYQRYATYK-KWH-FE-VLEYFPSEIGGLRHASASIGGSEVYRHMKFEGGVHRVQRVPKTEKQG
          T.EMFDMYQ.YATYK.KWH.FE..LEYFPSEI.G..HASASIGG...YR.M.FEG.VHRVQ.VPKTEKQ.
Retrocopy TAEMFDMYQQYATYK<KWH<FE<ILEYFPSEIDGPKHASASIGGPKAYRKMEFEGSVHRVQQVPKTEKQV

Parental  RMHTSTMTVAVLPQPSEINLVISPKDLRIETKRASGAGGQHVNTTDSAVRIVHLPT
          .MH.S.MT.AVL..P.EI.L.I.PK.L.IETK.AS.AG....NTTDSAVRI.HLPT
Retrocopy HMHNSIMTTAVLS*PPEISLIINPKSL*IETK*ASRAG----NTTDSAVRITHLPT

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_129 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012787	1 retrocopy	retro_cjac_1305,
Homo sapiens	ENSG00000112031	1 retrocopy	retro_hsap_3018,
Sarcophilus harrisii	ENSSHAG00000017997	1 retrocopy	retro_shar_129 ,
Ictidomys tridecemlineatus	ENSSTOG00000009980	1 retrocopy	retro_itri_335,
Tupaia belangeri	ENSTBEG00000003131	2 retrocopies	retro_tbel_2448, retro_tbel_4085,