RetrogeneDB ID: retro_itri_324

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:24524176..24524600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSSTOG00000013572
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_itri_324
GTGTTCACCTGTGCCACGCTCACCTGCACCCTTGCTCTGATTTGTGCTGGATCCAGAGGTGCAGCCCAGCCCATTTCTGC
CTCAGTATTATCTTCACCAGATAATACTGAGAGGCCTTGAGAGGACCCAACAGTTTTTAATGGGGCCTGGAATGGTGTGT
GTCAGCTAATCCGATGGGAGTTTCAAACCAGTGCAATCAGCAGAAACATTGGTACTGCTGCCACATTTATTGGTGCAAGG
TGCTGCAACAGCAAGAGCGGCTGGTTCTGGTGCTAGTATTGGAACAGTCTTTGGAAGCCTTATCCTTGGCAGAAACCCTT
TGCTGAAGCAGCAGCCATTCTTGTATGCCACCCTGGGATTTGCCTTGTTTGAAGCTACGGGTCTTTTTTGTTTGATGGTC
ATTTTCTTAATCTTGTTTGCCATA

Alignment

ORF - retro_itri_324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFACAKLACTPALIRAGSRVAYRPISVSVLSRPET--RPGKGSTVFNEAQNGERQLIRREFQTSVISRDI
          .F.CA.L.CT.ALI.AGSR.A..PIS.SVLS.P....RP....TVFN.A.NG..QLIR.EFQTS.ISR.I
Retrocopy VFTCATLTCTLALICAGSRGAAQPISASVLSSPDNTERP*EDPTVFNGAWNGVCQLIRWEFQTSAISRNI

Parental  DTAAKFIGA-GAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLI
          .TAA.FIGA.GAAT...AGSGA.IGTVFGSLI.G..RNP.LKQQ.F.YA.LGFAL.EA.GLFCLMV.FLI
Retrocopy GTAATFIGA>GAATARAAGSGASIGTVFGSLILG--RNPLLKQQPFLYATLGFALFEATGLFCLMVIFLI

Parental  LFAM
          LFA.
Retrocopy LFAI

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_324 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_324 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 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000008217	3 retrocopies	retro_itri_1404, retro_itri_399, retro_itri_436,
Ictidomys tridecemlineatus	ENSSTOG00000013404	2 retrocopies	retro_itri_1604, retro_itri_560,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324 , retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,