RetrogeneDB ID: retro_itri_249

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:29947443..29948279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSSTOG00000019553
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_itri_249
GATGCCATCCATCAAGGCATGGATGAGGAACTGGAAAGAGAGGAGAAATTATTTCCGCTTGGGGAAGAAGTGGCCCAGTA
TGACAGGACATGCAAGGTTAGCTGAGGCCTGTGGAAAAAATATGGACATGAGGATTATAGATACTCTCATATCTGAGACG
GGCTTTGCTAGAATTGCTGTCAGTGGAGCTATGGCTGGGTTGTGGCCCATTTGTGAATTTATGACCTTCAATTTCTCTGT
GCAAGCCACTGACCAGGTTATAAATTCAGCTGCCAAGACCTACTATATGCTGGGGGGCCTCCAGCCTGTGCCCATAGTCA
TAGGGAAGCCAGTGGCACCTCGGTGGGTGTGGCTGGCCAGAACTCACAGGGCTTTGCCACGTGGGATGGGAAGTCCTTAG
GCCTTAAAGGTGGTCATCCCCTGGAATTCAGAGGATGCAAAAAGGTTTTATTAACTCAGACATTGAGATAACAATCAGGG
ATAGTACTGGAAAATCAGTTGATGTATGGAGTTCCTTTTGAACTTCTTGCAGAAGCTCAGTCAAAGATTTTCTGGTTCAT
ATTGGAAAAGTCAAAATAGAAAGCCAAGGGACCGTGGTTTCCCACACAAGACCTGAGTGCCACTGCTGAGAAGTTGCAAC
GGTGCTGTCTAAAGAAGAAATTGAAGGTGAGGTGATCAGTATGGGTACCATCAGACCAATGGATGTTGAAACCATAGAAA
CCAACATTATGAAGACAAATTGTCTCTGAGCCCTGGAAGGAGGCTGGCCCCAGTTTGCAGCAGGAGCTAAAATTTGTGCC
AGGATCGTGGATGACCTTGCATTCAATTTCCTGGAT

Alignment

ORF - retro_itri_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 78.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DAINQGMDEELERDEKVF-LLGEEVAQYDGAYKVSRGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLR
          DAI.QGMDEELER.EK.F..LG.......G.........K...D.RIIDT.ISE.GFA.IAV..AMAGL.
Retrocopy DAIHQGMDEELEREEKLF>RLGKKWPSMTGHARLAEACGKNM-DMRIIDTLISETGFARIAVSGAMAGLW

Parental  PICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQCVPIVFRGP-NGASAGVAAQHSQCFAAWYGHCPG-LK
          PICEFMTFNFS.QA.DQVINSAAKTYYM.GGLQ.VPIV...P..G.S.GVA.Q.SQ.FA.W.G...G.LK
Retrocopy PICEFMTFNFSVQATDQVINSAAKTYYMLGGLQPVPIVIGKP<SGTSVGVAGQNSQGFATWDGKSLG>LK

Parental  VVSPWNSEDA-KGLIKSAIR-DNN-PVVVLENELMYGVPFEFPTEAQS-KDFLIPIGKAKVERQGTHITV
          VV.PWNSEDA.KG.I.S.I..DNN....VLEN.LMYGVPFE...EAQS.KDFL..IGK.K.E.QGT...V
Retrocopy VVIPWNSEDA>KGFINSDIE<DNN<SGIVLENQLMYGVPFELLAEAQS<KDFLVHIGKVKIESQGT---V

Parental  VSHSRPVGHCLEAATVLSKEGIECEVINMRTIRPMDIDTIEASVMKTNHLITVEGGWPQFGVGAEICARI
          VSH.RP..HC.E.ATVLSKE.IE.EVI.M.TIRPMD..TIE...MKTN.L...EGGWPQF..GA.ICARI
Retrocopy VSHTRPECHC*EVATVLSKEEIEGEVISMGTIRPMDVETIETNIMKTNCL*ALEGGWPQFAAGAKICARI

Parental  MEGPAFNFLD
          ....AFNFLD
Retrocopy VDDLAFNFLD

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_249 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_249 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249 ,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,