RetrogeneDB ID: retro_shar_97

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850125.1:928..1744(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000427
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000003493
• Aliases: None
• Description: None

Sequence

>retro_shar_97
TCCCGGATGGCGTTGAGCGCGGCGAGACTGGAGCCGGGCACCGAAGGGTTCGGCGTGACTTCTCCGCGGGAGCCCGAGCC
CGAGTCCGAGCCCGACTTCGCGCCGGCATCTTCGGGGCCGGGAGGGGAACTCGGAGGTGACGGGAAGCGAGTAATGCCCG
GCATCCTGTACCTGGGGCATATCCCGCCGCGCTTCCGGCCCCTGCATGTGCGGAACCTGCTCAGCGGTCACGGCGAAATC
GGTCGCGTCTTCTTCCAGCCGCAGGCCCGATCGGGCCGAGCGGGGAAAACCCGGAGCTGCCGCCGCTGGGGGCAGGACTA
CACCGAGGGCTGGGTGGAGTTCCGGGACAAGCGGGTGGCCAAGCTGGTGGCGGCCAGCCTGCACCACACGCCCATGGGCG
CCCAGCGCCGAAGCCCCTTCCGGTACGATCTGTGGAACCTCAAGTACTTGCACCGATTCAAGTGGAGCCATTTGAGCGAG
CGCCTGGCCTGTGAGCGGCAGGGGAGGCAGCAGCGCCTCCGGGCCGAGGTCGCCCAGGCCAAGCGCGAAACGGACTTTTA
CCTGCGGAGCGTGGAGAAGGGCAGACGTTTCCTGGAGAAGGCGGAAGTCGCGCTGGCCGCGGGCCAGGAGGAATCGGTCG
CGGCGGATAAGAGCTGGGGCTTCCTCCAGCGCCCCACGGAGATGGAGATCCGGAAGCACCGAGAAGAGATTCAGCCCGGC
CAGGGCAGGGACCAGCAACTCCAGATGCCCGAGTCTTCCAAGAAGGCTCAGCCGAACGAGTCGCTGCTAGCCAAGATCTT
CCGTCCTGCAGCCTGA

Alignment

ORF - retro_shar_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLSAVRPEPGSEGFGVSSPRELESESESDFVSASSEAGGELGADGKRVVPGIIYLGHIPPCFRPLHVRN
          M.LSA.R.EPG.EGFGV.SPRE.E.ESE.DF..ASS..GGELG.DGKRV.PGI.YLGHIPP.FRPLHVRN
Retrocopy MALSAARLEPGTEGFGVTSPREPEPESEPDFAPASSGPGGELGGDGKRVMPGILYLGHIPPRFRPLHVRN

Parental  LLSVHGEIGRVFFQPEDRSGRLKKTRSSSAGRRLRQAYTEGWVEFRDKRVAKLVVASLHNTPMGAQRRSP
          LLS.HGEIGRVFFQP..RSGR..KTRS....RR..Q.YTEGWVEFRDKRVAKLV.ASLH.TPMGAQRRSP
Retrocopy LLSGHGEIGRVFFQPQARSGRAGKTRSC---RRWGQDYTEGWVEFRDKRVAKLVAASLHHTPMGAQRRSP

Parental  YRYDLWNLKYLHRFKWSHLSERLAYERHVRQQRLRAEISQAKRETDFYLQSVEKSKHFQKKAKAALASRG
          .RYDLWNLKYLHRFKWSHLSERLA.ER..RQQRLRAE..QAKRETDFYL.SVEK...F..KA..ALA...
Retrocopy FRYDLWNLKYLHRFKWSHLSERLACERQGRQQRLRAEVAQAKRETDFYLRSVEKGRRFLEKAEVALAAGQ

Parental  EGSVAAEKSWGFIQRPTEMEIRKHR-EIPTSQAREQQMQTQIHEFARKAQPNEPLLAKIFRPGA
          E.SVAA.KSWGF.QRPTEMEIRKHR.EI...Q.R.QQ...Q..E...KAQPNE.LLAKIFRP.A
Retrocopy EESVAADKSWGFLQRPTEMEIRKHREEIQPGQGRDQQL--QMPESSKKAQPNESLLAKIFRPAA

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_97 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005188	1 retrocopy	retro_chof_1748,
Cavia porcellus	ENSCPOG00000008937	1 retrocopy	retro_cpor_1386,
Gorilla gorilla	ENSGGOG00000024149	1 retrocopy	retro_ggor_2106,
Macaca mulatta	ENSMMUG00000006914	1 retrocopy	retro_mmul_1959,
Otolemur garnettii	ENSOGAG00000026316	1 retrocopy	retro_ogar_2895,
Pongo abelii	ENSPPYG00000016335	1 retrocopy	retro_pabe_2541,
Rattus norvegicus	ENSRNOG00000017585	1 retrocopy	retro_rnor_841,
Sarcophilus harrisii	ENSSHAG00000003493	1 retrocopy	retro_shar_97 ,