RetrogeneDB ID: retro_itri_758

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393318.1:11707908..11708233(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSSTOG00000007542
• Aliases: None
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_itri_758
GGGACTGTGATTGTCAGGTGCAGCCTTGACTCCCTGCTGGGCCTCTACTTCCTCTCCCACATCCCCATCACTCTGTTTTT
GGACCTGCAGGCTGAACTGCTGTGAGAATTCTACTGGGTCAAGTTCAGAAACCTGCTGACTTGGTATGCTAAAGAGTTTA
AAGACCCTCTGATGAAGATCACCCCAGTGTGGTTTAAATCCTTGTGTTTCGTGAGCTTTTGTTTCAGCTGCCTTTCTTTC
ACTTTGCAACATATGTCTTCTTCCAAGAAATTGCAAGTGGATCCGCATGCCTGCAATCATCTGCTCAGTTCACATCCTGA
CAACA

Alignment

ORF - retro_itri_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.07 %
• Parental protein coverage: 62.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTMIVKRSIDFLLGFYFLSHIPITLFLDLQVVLPRQLYSVKLRNLLAWYAEEFKDPLIQSTPVWFQS-FV
          GT.IV..S.D.LLG.YFLSHIPITLFLDLQ..L....Y.VK.RNLL.WYA.EFKDPL...TPVWF.S..V
Retrocopy GTVIVRCSLDSLLGLYFLSHIPITLFLDLQAELL*EFYWVKFRNLLTWYAKEFKDPLMKITPVWFKS<LV

Parental  FCELLFQLPFFPAATYAFFK-GNCKWIRMPAIIYSVHTLTT
          F.ELLFQLPFF..ATY.FF...NCKWIRMPAII.SVH.LTT
Retrocopy FRELLFQLPFFHFATYVFFQ<RNCKWIRMPAIICSVHILTT

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_758 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_758 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758 ,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,