RetrogeneDB ID: retro_shar_212

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834674.1:1145502..1145741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D2
• Ensembl ID: ENSSHAG00000018938
• Aliases: None
• Description: SFT2 domain containing 2 [Source:HGNC Symbol;Acc:25140]

Sequence

>retro_shar_212
TTTCCTGCTTATTTTTCTATAGGGATTCTTTTCTTGTTCCTGGATACCTTTTTGTTATGGGTGCCTTGAAAAGGACTTAT
CTTTTTTGCAGAATTTTATGCCTTGTAGAACACTGCATCACTTGACACTATTCTTTCTTATGGGATAATGAAACAGCTGA
AATTTATATTTAAGACTATTTGACGATATCCACCACTGGAATGCTATTGCATCTTGTATTTACTCTGTGTTCTGCCTTC

Alignment

ORF - retro_shar_212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.32 %
• Parental protein coverage: 57.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAACFAIGIVFSLMGTFLLWVPRKGLVLFAAFYTLGNIASLGSTIFLMGPMKQLKRMFEPT-RLIATIVM
          F.A.F.IGI.F....TFLLWVP.KGL..FA.FY.L.N.ASL..TI...G.MKQLK..F......I.T..M
Retrocopy FPAYFSIGILFLFLDTFLLWVP*KGLIFFAEFYAL*NTASL-DTILSYGIMKQLKFIFKTI<LTISTTGM

Parental  LLCLALTLCSAF
          LL.L..TLCSAF
Retrocopy LLHLVFTLCSAF

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_212 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212 ,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133,