RetrogeneDB ID: retro_itri_699

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:4350194..4350387(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMIM20
• Ensembl ID: ENSSTOG00000004810
• Aliases: None
• Description: small integral membrane protein 20 [Source:HGNC Symbol;Acc:37260]

Sequence

>retro_itri_699
CAAAACCTGCACACCTTGCTCATTTTTGGCTGTTTGGTCTCCCTTTTGGGGCTGCCTTCTATTGCATCTACTTCTGCCTC
CTAATGAGGCTGGAGGAATACCAGAAGAAACAAGTCATAAATCAGGCCAATATTGTTCAATAAGATGTACAGCCACAGGG
TTAAGAATGTGGTCTTATCCATTCAGCAGGAAA

Alignment

ORF - retro_itri_699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 95.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNLRTALIFGGFVSLVG-AAFYPIYFRPLMRLEEYQKEQAINRAGIVQEDVQP-PGLKVWSDPFGRK
          .NL.T.LIFG..VSL.G.AAFY.IYF..LMRLEEYQK.Q.IN.A.IVQ.DVQP..GL..WS.PF.RK
Retrocopy QNLHTLLIFGCLVSLLG<AAFYCIYFCLLMRLEEYQKKQVINQANIVQ*DVQP<TGLRMWSYPFSRK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_699 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_699 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003897	1 retrocopy	retro_btau_95,
Dasypus novemcinctus	ENSDNOG00000004966	2 retrocopies	retro_dnov_1474, retro_dnov_1529,
Macropus eugenii	ENSMEUG00000002680	1 retrocopy	retro_meug_147,
Microcebus murinus	ENSMICG00000017222	1 retrocopy	retro_mmur_868,
Macaca mulatta	ENSMMUG00000006680	1 retrocopy	retro_mmul_179,
Nomascus leucogenys	ENSNLEG00000016894	1 retrocopy	retro_nleu_216,
Ictidomys tridecemlineatus	ENSSTOG00000004810	1 retrocopy	retro_itri_699 ,
Tupaia belangeri	ENSTBEG00000015052	2 retrocopies	retro_tbel_1277, retro_tbel_4083,