RetrogeneDB ID: retro_itri_1529

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393527.1:2378369..2379143(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSSTOG00000015433
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_itri_1529
AGGAAGATGCTGGCCACCACGGTGTCCCACGTGCTGTCGGGACTCACTCAGAAGCTGGCTTGCAGAGGGCTGCTGGCTTC
TTGTAACTTTTCAAAAGAAGTTACGTTTGAAATTAAGAGCTGTGATCTTTAGGGGTTGGAAGAGGGTCCTCCTGTAGCAA
CAGTACTCACCAGGGAGGATGGGACCGAATACGACAGGACAATGCAGGTGGTTTCCCGCAGGGGAACTGATCAGCTGTAT
AAACAGAAATGTATTTACGGTTTGTGTCACTTGTGTGCGGGTCAGGAAGCTTGCTACGTGGGGCTTGAGGCAGGAATAAA
GCCCTGGGATCATGTCATCACATCCTATCATGGCATAGGCTACACCTGGGGACTTAGCATGGGATCTGTTCTGGCAGATC
TGACTGCTCCAAGAGGAGGTTGTGCTAAAGAAAAGTGAGGCTGCATGCACTTGTATTCCAGTAAGTTCTATGGGGGCAAT
GGCATTGTGGGGGCGCAGGTGCCCCTAGGAGCTGGTGTCGCCCTGGCCTGTAACCATGTGGGAAACGATGAGATCTGTTT
GATTTTATATGGGGATGGTGCTGCTAATCAGGGCCAGATAGCAGAAGCACACAATGTGGCAGCCTTGTGGAAATTACTCT
GTGTTCTCATCTGTGAGAATCGTCTCTATGGATTGGGGACATCTGTTGAGAGAGCATCAGCCAACACGGAATATTACAAG
AGAGACAATTTTATGCCTGGGCTGTGGGTAGATGGGCTGGACATTCGAAGTGTG

Alignment

ORF - retro_itri_1529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.56 %
• Parental protein coverage: 66.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKMLAA-VSRVLAGAAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQT
          RKMLA..VS.VL.G..QK.A.R.L.AS.NF....TFEIK.CDL..LEEGPPV.TVLTREDG..Y.R.MQ.
Retrocopy RKMLATTVSHVLSGLTQKLACRGLLASCNFSKEVTFEIKSCDL*GLEEGPPVATVLTREDGTEYDRTMQV

Parental  VRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTG
          V.R.....DQLYKQK.I.G.CHLC.GQEAC.VGLEAGI.P.DH.IT.Y..HG...T.GLS....LA.LT.
Retrocopy VSRRG--TDQLYKQKCIYGLCHLCAGQEACYVGLEAGIKPWDHVITSY--HGIGYTWGLSMGSVLADLTA

Parental  RRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNM
          .RGGCAK.K.G.MH.Y...FYGGNGIVGAQVPLGAG.ALAC...G.DE.CL.LYGDGAANQGQI.EA.N.
Retrocopy PRGGCAKEK*GCMHLYSSKFYGGNGIVGAQVPLGAGVALACNHVGNDEICLILYGDGAANQGQIAEAHNV

Parental  AALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCV
          AALWKL.C..ICEN..YG.GTSVERA.A.T.YYKR..F.PGL.VDG.DI..V
Retrocopy AALWKLLCVLICENRLYGLGTSVERASANTEYYKRDNFMPGLWVDGLDIRSV

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_1529 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1529 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 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016730	1 retrocopy	retro_amel_400,
Bos taurus	ENSBTAG00000019852	2 retrocopies	retro_btau_100, retro_btau_1807,
Callithrix jacchus	ENSCJAG00000005496	2 retrocopies	retro_cjac_2414, retro_cjac_27,
Dipodomys ordii	ENSDORG00000011848	1 retrocopy	retro_dord_35,
Equus caballus	ENSECAG00000001964	1 retrocopy	retro_ecab_21,
Erinaceus europaeus	ENSEEUG00000005485	1 retrocopy	retro_eeur_580,
Homo sapiens	ENSG00000131828	1 retrocopy	retro_hsap_41,
Gorilla gorilla	ENSGGOG00000013574	1 retrocopy	retro_ggor_59,
Myotis lucifugus	ENSMLUG00000012932	2 retrocopies	retro_mluc_2363, retro_mluc_323,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Mustela putorius furo	ENSMPUG00000003269	1 retrocopy	retro_mputfur_812,
Mus musculus	ENSMUSG00000031299	2 retrocopies	retro_mmus_63, retro_mmus_631,
Nomascus leucogenys	ENSNLEG00000009805	1 retrocopy	retro_nleu_74,
Oryctolagus cuniculus	ENSOCUG00000014748	1 retrocopy	retro_ocun_264,
Pongo abelii	ENSPPYG00000020171	1 retrocopy	retro_pabe_129,
Pan troglodytes	ENSPTRG00000021717	1 retrocopy	retro_ptro_79,
Pteropus vampyrus	ENSPVAG00000005420	1 retrocopy	retro_pvam_1306,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,
Sus scrofa	ENSSSCG00000023643	2 retrocopies	retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus	ENSSTOG00000015433	1 retrocopy	retro_itri_1529 ,
Tupaia belangeri	ENSTBEG00000014313	1 retrocopy	retro_tbel_3327,
Tursiops truncatus	ENSTTRG00000000660	1 retrocopy	retro_ttru_1427,