RetrogeneDB ID: retro_dord_329

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_11841:34651..35713(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000007661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tkt
• Ensembl ID: ENSDORG00000001392
• Aliases: None
• Description: transketolase [Source:MGI Symbol;Acc:MGI:105992]

Sequence

>retro_dord_329
GAAGAGCAAGCCGATGCAGTTATCGCATCCCTGGAGAGTCAAATAAGATCCAACCGCCATCTCACACCCAAGGCCCCCGT
GGAAGACTCGCCGCAGATCAACACCAATAACGTGAAAATGGCCTCGCCTCCTGCTTACAGACTGGGCGAGAAGATAGCCA
CCGGAAAAGCCTCTGGTTTGGCCCTGGCTAAACTGGGCCATGCTCACAAAAGAGTTATTGTTTTGGACTGTGACCCGAAA
AACTCCATCTACTCCGAGATTTTCAAGAAAGAGCATCCGGAGCGCTACATAGAGTGTCTGATGGCCGAGCAGAACATGGT
GAGCGTGGCTCTGGGGTGTGCTACCCGAGGGCGGACCATTGCCTTTGCCAGTACCTTTGCTGCCTTTTTCACCCGCGCCT
TCGATCAGATCCGAATGGGTGCCATCTCGGACACCAACATCAATCTGATTGGTTCTCACTGCGGGGTGTCCTTTGGTGAA
GATGGACCCTACCAGATGGCGCTAGAGGACCTGGCCATGTTCCGAAGCATTCCCAATTGCACCATCTTCTATCCAAGCGA
TGCCGTCTCCACGGAGCACGCTGTTTATCTGGCTGCCAGTACCAAGGGAATGTGCTTCATTCGGACCAGTCAGCCGGAAA
CTGCAGTGATCTATACCCCACATGAACCTTTTGAGGTCGGACAGGCCAAGGTCATCCACCAGAGTGCCCAGGACAAGGTG
ACAGTTATCGGAGCTGGAGTTACTCTCCATGAAGCCTTAGCAGCTGCTGATGATCTTTTCCAGCAAGGCATTTCTGTTCG
TGTCATTGACCTATTCACCATTAAACCATTGGATGCTGCCACCATCATCTCCAGTGCAAAAGCCACAGGTGGCCGGATTA
TCACTGTGGAAGACCACTATCTAGAAGGTGGCATTGGAGAAGCTGTGTGTGCAGCCGTCTCCGGAGAGCCCGACATCCAC
GTTCATCGGCTGGCGGTGACGGAGCTGCCTCGAAGTGGGAAACCTGGGGAATTGCTGGATATGTTTGGAATCAGTGCCAG
ACACATCATAGCAGCTGTGAAA

Alignment

ORF - retro_dord_329 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 60.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNMAEQIIQEIFSQVQSKKKILATPPQEDAPSVDIANIRMPTPPSYKVGDKIATRKAYGQALAKLGHASD
          ...A...I....SQ..S........P.ED.P.....N..M..PP.Y..G.KIAT.KA.G.ALAKLGHA..
Retrocopy EEQADAVIASLESQIRSNRHLTPKAPVEDSPQINTNNVKMASPPAYRLGEKIATGKASGLALAKLGHAHK

Parental  RIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRNRTVPFCSTFAAFFTRAFDQIRMA
          R.I.LD.D.KNS..SEIFKKEHP.R.IEC..AEQNMVS.A.GCATR.RT..F.STFAAFFTRAFDQIRM.
Retrocopy RVIVLDCDPKNSIYSEIFKKEHPERYIECLMAEQNMVSVALGCATRGRTIAFASTFAAFFTRAFDQIRMG

Parental  AISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSIPMSTVFYPSDGVATEKAVELAANTKGICFIRTS
          AIS..NINL.GSHCGVS.GEDGP.QMALEDLAMFRSIP..T.FYPSD.V.TE.AV.LAA.TKG.CFIRTS
Retrocopy AISDTNINLIGSHCGVSFGEDGPYQMALEDLAMFRSIPNCTIFYPSDAVSTEHAVYLAASTKGMCFIRTS

Parental  RPENAIIYNNNEDFQVGQAKVVLKSKDDQVTVIGAGVTLHEALAAAELLKKEKINIRVLDPFTIKPLDQK
          .PE.A.IY...E.F.VGQAKV...S..D.VTVIGAGVTLHEALAAA..L....I..RV.D.FTIKPLD..
Retrocopy QPETAVIYTPHEPFEVGQAKVIHQSAQDKVTVIGAGVTLHEALAAADDLFQQGISVRVIDLFTIKPLDAA

Parental  LILESARATKGRILTVEDHYYEGGIGEAVSTAVMGEPGVTVTRLAVGQVPRSGKPAELLKMFGIDKDAIV
          .I..SA.AT.GRI.TVEDHY.EGGIGEAV..AV.GEP...V.RLAV...PRSGKP.ELL.MFGI....I.
Retrocopy TIISSAKATGGRIITVEDHYLEGGIGEAVCAAVSGEPDIHVHRLAVTELPRSGKPGELLDMFGISARHII

Parental  QAVR
          .AV.
Retrocopy AAVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_329 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003758	1 retrocopy	retro_btau_176,
Callithrix jacchus	ENSCJAG00000007253	1 retrocopy	retro_cjac_2128,
Cavia porcellus	ENSCPOG00000000072	1 retrocopy	retro_cpor_45,
Dipodomys ordii	ENSDORG00000001392	1 retrocopy	retro_dord_329 ,
Homo sapiens	ENSG00000163931	1 retrocopy	retro_hsap_47,
Macropus eugenii	ENSMEUG00000005312	3 retrocopies	retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus	ENSMLUG00000000943	1 retrocopy	retro_mluc_67,
Macaca mulatta	ENSMMUG00000014433	1 retrocopy	retro_mmul_74,
Mus musculus	ENSMUSG00000021957	1 retrocopy	retro_mmus_220,
Oryctolagus cuniculus	ENSOCUG00000015904	2 retrocopies	retro_ocun_319, retro_ocun_62,
Otolemur garnettii	ENSOGAG00000016911	1 retrocopy	retro_ogar_5,
Ochotona princeps	ENSOPRG00000009891	1 retrocopy	retro_opri_10,
Pan troglodytes	ENSPTRG00000015024	1 retrocopy	retro_ptro_126,
Pteropus vampyrus	ENSPVAG00000016283	1 retrocopy	retro_pvam_352,
Rattus norvegicus	ENSRNOG00000016064	1 retrocopy	retro_rnor_146,
Sarcophilus harrisii	ENSSHAG00000017349	1 retrocopy	retro_shar_827,
Sus scrofa	ENSSSCG00000021408	1 retrocopy	retro_sscr_996,
Tupaia belangeri	ENSTBEG00000012114	1 retrocopy	retro_tbel_3510,
Takifugu rubripes	ENSTRUG00000003009	1 retrocopy	retro_trub_23,