RetrogeneDB ID: retro_shar_332

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841368.1:103020..103538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010459
• Aliases: None
• Description: None

Sequence

>retro_shar_332
CTTCCAGATAAGTCAGACCACAACATGCCACACAGTGGCTCTGGAGGCGGGCCCGGTGTTGAGACCGGAGCCAAATTGCT
GATCTCCACTCTGGATTGTGGAGTCTCGGATGCGGATATTCAGGAACTATTTGCTGCGTTTGGAACTCTAAGAAGGCAGC
TGTACATTATGATCCATCCAGCCGAAGCTTAGGAACAGCAGATGTTCACTTTGAGCGAAAAGCAGATGCTCTGAAGGGCT
TGAAACACTATAATGGTGTCCTTTTGGATGGTAACCCTATAAACATTTAGCTTCTTATATCACAGACTGATACACATGGA
AGACCTGCATAGAATGTAAATAGAGGTGAAATGATTGGAAATCGTAGCTCTGGAGGTTTTGGTAGTGGAGGTGGCACCCA
GAGAGGCGGTCGTGGAGGCAATCGAGGATGAGGTCGAGGGACTGGAAGAAATTCGAAACAACAGCTTCCCATAGAAGAAC
TAGATGCACAAGTGGATGCTTATAATGCCATGATTGAA

Alignment

ORF - retro_shar_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 89.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTL-KKAAVHYDRSGRSLGTADV
          LPDK..H....SG.GGG.GVETG.KLL.S.LD.GVSDADIQELFA.FGTL.KKAAVHYD.S.RSLGTADV
Retrocopy LPDKSDHNMPHSGSGGGPGVETGAKLLISTLDCGVSDADIQELFAAFGTL<KKAAVHYDPSSRSLGTADV

Parental  HFERKADALKAMKQYNGVPLDGRPMNIQLVTSQIDTQRRPAQSVNRGGMTRNRGSGGFGGGGGTRRGSRG
          HFERKADALK..K.YNGV.LDG.P.NI.L..SQ.DT..RPA..VNRG.M..NR.SGGFG.GGGT.RG.RG
Retrocopy HFERKADALKGLKHYNGVLLDGNPINI*LLISQTDTHGRPA*NVNRGEMIGNRSSGGFGSGGGTQRGGRG

Parental  GNRGRGRGTGRNSKQQLSAEELDAQLDAYNARMD
          GNRG.GRGTGRNSKQQL..EELDAQ.DAYNA...
Retrocopy GNRG*GRGTGRNSKQQLPIEELDAQVDAYNAMIE

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_332 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005877	1 retrocopy	retro_cfam_1395,
Gorilla gorilla	ENSGGOG00000013935	1 retrocopy	retro_ggor_2523,
Macaca mulatta	ENSMMUG00000012884	1 retrocopy	retro_mmul_1679,
Mus musculus	ENSMUSG00000025134	1 retrocopy	retro_mmus_286,
Sarcophilus harrisii	ENSSHAG00000010459	1 retrocopy	retro_shar_332 ,
Tupaia belangeri	ENSTBEG00000005834	7 retrocopies	retro_tbel_237, retro_tbel_2432, retro_tbel_251, retro_tbel_2690, retro_tbel_2918, retro_tbel_3933, retro_tbel_3934,