RetrogeneDB ID: retro_itri_1162

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393390.1:5458632..5459512(-)
• Located in intron of: ENSSTOG00000001768

Retrocopy information

• Ensembl ID: ENSSTOG00000019799
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAS7
• Ensembl ID: ENSSTOG00000022185
• Aliases: None
• Description: growth arrest-specific 7 [Source:HGNC Symbol;Acc:4169]

Sequence

>retro_itri_1162
TGCGTGACATTCCCTCACCCAGACACCATGCCTGAACAGCAACTGCTAAAGCCAACCGAGTGGAGCTACTGTGACTACTT
TGGGACTGATAAGAAGGATCCCCAAGGCAATGGCACGGTGGCTGGGTTGGAATTGCTGCTCCAAAAGCAACTGAAAGGCA
AACAAACATGAAAGAAATGTCTGAATTCGTCCGAGAGAGGAGAAAGATTGAAGAAAAATATGCAAAGAACTTGGCTAAGC
TCTCTCAGAACTCCTTGGCTGCACAGGAGGAAGGCTCCTTGGGAGAAGCCTGGGCCCAGGTGAAGAAGAATCTGGCAGAT
GAAGCAGAAGTTCATATCAAGTTCTCTGCCAAGCTTAACAGCGAGGTAGAGAAGCCCCTAATGAACTTTCGTGAGAACTT
CAAGAAAGACATGAAAAAGTGTGACCACCATATCGCTGACCTTCGCAAGCAGCTCGCCAGCCGCCATGCATCGGTGGAGA
AGGCCCAGAAAGCCCTCACAGAGCAGCAGAGAGACCTGGAGATGAAGACCCAGCAACTGGAGATCAAGCTGAGCAACAAG
ACAGAGGAGGACATCAAGAAGGCCCGGAGAAAGTCCACACAGGCTGGCGATGACCTCATGCGCTGTGTGGACCTCTACAG
CCAGGCACAGTCCAAGTGGTTTGAAGAGATGGTGACCACCACTTTGGAGCTGGAGCGGCTGGAGATATCTGGCAACATCT
GTATCAGTACACACAGCTGTAGCATGAGACAGACATGTTCAACCAAAGCACAGTACAGCCTGTGGACCAACTGCTTCGAA
AAGTGGACCCGGCCAAAGACAGAGAGCTGTGGGTCAGAGAGCACAAAATGGGCAACATTCGCCCCGTGGACATGAAGATC

Alignment

ORF - retro_itri_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.05 %
• Parental protein coverage: 71.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFELLLQKQLKGKQM-QKEMSEFVRERIK
          CVTFPHPDTMPEQQLLKPTEWSYCDYF..DKKDPQGNGTVAG.ELLLQKQLKGKQ...KEMSEFVRER.K
Retrocopy CVTFPHPDTMPEQQLLKPTEWSYCDYFGTDKKDPQGNGTVAGLELLLQKQLKGKQT<MKEMSEFVRERRK

Parental  IEEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMK
          IEE.YAKNLAKLSQNSLAAQEEGSLGEAWAQVKK.LADEAEVH.KFSAKL.SEVEKPLMNFRENFKKDMK
Retrocopy IEEKYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKNLADEAEVHIKFSAKLNSEVEKPLMNFRENFKKDMK

Parental  KCDHHIADLRKQLASRYASVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMRC
          KCDHHIADLRKQLASR.ASVEKA.KALTE.QRD..............KTEEDIKKARRKSTQAGDDLMRC
Retrocopy KCDHHIADLRKQLASRHASVEKAQKALTEQQRDXXXXXXXXXXXXXXKTEEDIKKARRKSTQAGDDLMRC

Parental  VDLYNQAQSKWFEEMVTTTLELERLEVERVEM-IRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPAK
          VDLY.QAQSKWF.E...TT.....LE.ER.E..I.QHL.QYTQL.HETDMFNQSTV.PVDQLLRKVDPAK
Retrocopy VDLYSQAQSKWF-EEMVTTT----LELERLEI<IWQHLYQYTQL*HETDMFNQSTVQPVDQLLRKVDPAK

Parental  DRELWVREHKTGNIRPVDMEI
          DRELWVREHK.GNIRPVDM.I
Retrocopy DRELWVREHKMGNIRPVDMKI

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_1162 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1162 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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022185	12 retrocopies	retro_itri_1040, retro_itri_1162 , retro_itri_1203, retro_itri_1216, retro_itri_1416, retro_itri_1672, retro_itri_1733, retro_itri_282, retro_itri_294, retro_itri_372, retro_itri_466, retro_itri_762,