RetrogeneDB ID: retro_itri_1799

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393809.1:63576..63940(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012205
• Aliases: None
• Description: None

Sequence

>retro_itri_1799
GGCAATCTGATAGGCCACTACATCATGAATCATTAAAAATGACTGAAGCTGAGACCAATTCTTGGGTCCAATATGTAGGC
TCCGCTCAGGAGTCAGGCCACAGCAGCAGTTTTTAGTCATGAAATAAACAAATCTCTGGCTGTAGAGGGACTATATTCAG
AATAAAATAAGGGCCAGAAGAATGGAGAACAATAAGACATCACTAGCCTTCCACAGACTTTTCTCAGTCATAGGTGACAT
TGCAGAAAACAGTGTGGAGAATCAAGATAAGCAGAAACCTGAACCATACAGTCATGATAATAAAATAAATGAAGTGACAC
AAGGTGATAGACTCTGGACCCTGAAAAGCCAAAAACAATTAAAA

Alignment

ORF - retro_itri_1799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 65.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTLIACYIMKH-YRMTAAETIAWVR-ICRPGSVIGPQQQFLVMKQASLWIEGDYFRQKLRGQENGAHRTA
          G.LI..YIM.H...MT.AET..WV..ICR..S...PQQQFLVMK...LW...DY...K.R........T.
Retrocopy GNLIGHYIMNH<LKMTEAETNSWVQ<ICRLRSGVRPQQQFLVMK*TNLWL*RDYIQNKIRARRMENNKTS

Parental  AAFSRLLSGVDDISINGVENRDKQEPEPYSDDEEISGVTQGDRLRALKSRRQSK
          .AF.RL.S...DI..N.VEN.DKQ.PEPYS.D..I..VTQGDRL..LKS..Q.K
Retrocopy LAFHRLFSVIGDIAENSVENQDKQKPEPYSHDNKINEVTQGDRLWTLKSQKQLK

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_1799 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1799 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000081377	2 retrocopies	retro_hsap_3729, retro_hsap_3845,
Macaca mulatta	ENSMMUG00000005997	1 retrocopy	retro_mmul_1615,
Nomascus leucogenys	ENSNLEG00000016822	1 retrocopy	retro_nleu_1981,
Pongo abelii	ENSPPYG00000019417	1 retrocopy	retro_pabe_208,
Pan troglodytes	ENSPTRG00000021155	2 retrocopies	retro_ptro_2524, retro_ptro_2621,
Ictidomys tridecemlineatus	ENSSTOG00000012205	1 retrocopy	retro_itri_1799 ,
Ictidomys tridecemlineatus	ENSSTOG00000027626	1 retrocopy	retro_itri_1825,