RetrogeneDB ID: retro_itri_801

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393325.1:10194259..10195018(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000000386
• Aliases: None
• Description: None

Sequence

>retro_itri_801
AAGTTCAACTGCCCCTTCTTTGATGAAGGTTTTATTGCCAAGGACATTCTGAACCAAAAAAAAAAATCATGAAGTGTCTT
CTGATGATAAGAATGCCTTTTATGTTACAAACCATGGAGACTTGCTAAAGAAACATCTAAGATGATTAAAAGCTCTTCCC
CATGTCACCCCCTTTTATGCAGTCAAATTCAATGCTAACAGAGCTATAGGGAAGACTTTAGATGCCATTGGGATAGGATG
TGACTGTGCTAGCAAGACTGAAATATAGTTGGTGCAGAGTGTCCAAATGCCTCCAGAAAGAATTATCTATGCAAATCCTG
ATAAACAAGTTGTCTCAAATTAAATGTGCTGCCAGTATTGGAATCAAATGATGACTTATGACATTGAAGTCAAGTTGATG
AAATTTGCCAGAGAGCATCCAAAGGCAAAGTTGGTTTTGCAGATTGCCACTGATGATTCCAAAGCCGTCTGTTGCCTCAG
TGTTAAATTTGGTGCCACACTTAAAACCAGCAGAATTTCTTTTGGAACAAGCTAAAGAATGAAATGTTGATGTCATTTTG
TGTCAGCTTTCACGTGGGGAGTGGCTGCAGTGATCCTGAGACCTTCATGCAGGCCATCTCTGATGCCCACTGTGTCTTTA
ACATAGGAGCTGATGTTGATGTCAGCATGCATTTGCTTGATATTTGTGGTGACTTTCCTCAATGTGAGGATGTGAGGCTT
AAATATGAAGAGATCACCAGTGCGATCAACCCAGCACTA

Alignment

ORF - retro_itri_801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.93 %
• Parental protein coverage: 54.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EFDCHFLDEGFTAKDILDQKINEVS-SSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSRAI
          .F.C.F.DEGF.AKDIL.......S.SSDDK.AFYV...GD.LKKHLR.LKALP.VTPFYAVK.N..RAI
Retrocopy KFNCPFFDEGFIAKDILNXXXXS*S>SSDDKNAFYVTNHGDLLKKHLR*LKALPHVTPFYAVKFNANRAI

Parental  VKTLAAIGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQV-SQIKYAASIGV-QMMTFDSEVELMKVAR
          .KTL.AIG.G.DCASKTEI.LVQS...PPERIIYANP.KQV.SQIK.AASIG..QMMT.D.EV.LMK.AR
Retrocopy GKTLDAIGIGCDCASKTEI*LVQSVQMPPERIIYANPDKQV>SQIKCAASIGI<QMMTYDIEVKLMKFAR

Parental  AHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRL-LLERAKELNIDVI-GVSFHVGSGCTDPETFVQAI
          .HPKAKLVL.IATDDSKAVC.LSVKFGATLKTSR..LLE.AKE.N.DVI..VSFHVGSGC.DPETF.QAI
Retrocopy EHPKAKLVLQIATDDSKAVCCLSVKFGATLKTSRI>LLEQAKE*NVDVI>CVSFHVGSGCSDPETFMQAI

Parental  SDARCVFDMGAEAGFSMRLLDIGGGFPGSEDVKLKFEEITSVINPAL
          SDA.CVF..GA....SM.LLDI.G.FP..EDV.LK.EEITS.INPAL
Retrocopy SDAHCVFNIGADVDVSMHLLDICGDFPQCEDVRLKYEEITSAINPAL

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_801 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_801 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 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801 ,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,