RetrogeneDB ID: retro_shar_425

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842086.1:69151..69502(+)
• Located in intron of: ENSSHAG00000000524

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSSHAG00000011497
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_shar_425
TTTACAGCAATGAGAGATTTATACATGAAAAATGGACAAGGCTTTGCATTGGTCTACTCCATCATAGCACAGTCCACATT
TAATGATTTACAAAATCTTTGAGAACAGATACTTCGAGTTAAAGATACTGATGATATGCCAATGATTCTTGTTGGTAATA
AGTGTGACCTGGAAGATAAAAGAGTTGTAGGTAAAGAGCAAGGACAGAACCTAGCAAGACAATGGAACAACTGTGCATTC
TTAGAATCTTCCGCTAAATCAAAGATAAACATCAATGAGATCTTTTATGACCTAGTATGGCAAATTAACAGAAAAACTCC
AGTGCCTAGGAAGGCACATAAAAAGTCTTCA

Alignment

ORF - retro_shar_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 63.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQN
          FTAMRDLYMKNGQGFALVYSI.AQSTFNDLQ.L.EQILRVKDTDD.PMILVGNKCDLED.RVVGKEQGQN
Retrocopy FTAMRDLYMKNGQGFALVYSIIAQSTFNDLQNL*EQILRVKDTDDMPMILVGNKCDLEDKRVVGKEQGQN

Parental  LARQWNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSS
          LARQWNNCAFLESSAKSKIN.NEIFYDLV.QINRKTPVP.KA.KKSS
Retrocopy LARQWNNCAFLESSAKSKININEIFYDLVWQINRKTPVPRKAHKKSS

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_425 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425 ,
Sarcophilus harrisii	ENSSHAG00000012747	1 retrocopy	retro_shar_648,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,