RetrogeneDB ID: retro_dord_35

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_21334:4563..5727(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000013480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pdha1
• Ensembl ID: ENSDORG00000011848
• Aliases: None
• Description: pyruvate dehydrogenase E1 alpha 1 [Source:MGI Symbol;Acc:MGI:97532]

Sequence

>retro_dord_35
ATGCTGGCTTCTGTGGTCTCCCGCGTGTTGGGGGCCACCCAGAAGCCCCCTCTCAGAGTACTGCTGACCTCCTGCAACTA
TTCCAAGGATGCTACCATTGACATTAAGAGCTGCGATCTTTACCGGCTGGAGGGGGGCCCCGCGTCCTCCACCTTGCTAA
CCCGGGACGACGGGCTCAAGTACTACCGGGCCATGCAGATCGTTCGCCGGATGGAACTGAAGGCGGACCAGCTCTACAAA
CAGAAATTTATCCGTGGCTTCTGCCACCTGTGCGACGGCCAGGAAGCTTGCTGCGTGGGGATCGAGGCGGCCATCAAGCC
CACGGATAACGTGATCACCTCCTACCGGGCGCATGGCATCTGCTACACGCGCGGACTCTCGGTCAAGTCGATCCTGGCGG
AGCTGACGGGGCGCAGGGGAGGATGCGCCAAAGGCAAGGGCGGCTCCATGCACATGTACGCCAAGCACTTCTTCGGGGGC
AACGGCATCGTGGGCGCGCAGGTGCCCCTGGGCGCGGGGATCGCCCTGGCCTGCAAGTACCTGGGGAAACGGGACATCTG
CCTGGCCATGTATGGCGACGGAGCTGCCAACCAGGGCCAGATCGCCGAGGCCTACAACATGGCAGCGCTGTGGAAGCTGC
CGTGCGTGTTTATCTGCGAGAACAACCGCTACGCCATGGGCACGGCGGTGGAGAGGGCGGCGGCCAGCACCGATTACTAC
AAGCGGGGCAACTTCATCCCGGGCCTCAAGGTGAACGGCATGGATGTGCTGTGCGTGCGCGAGGCCACCAGGTTCGCGGC
GGATCACTGCCGGGCCGGGAAGGGCCCCATCGTGATGGAGCTGCAGACCTACCGGTACCACGGGCACAGCATGAGCGACC
CGGGCGTGAGCTACCGCACACGCGAGGAGATCCAGACCATGAGGAGCAAGAGCGACCCCATCATGCTGCTCCAGGAGAAG
ATGATCAGCCACAAGCTCAGCAGCGTGGAGGAGCTCAAGGAGATCGATGTGGAGGTGAGGAAGGAGATCGAGGAGGCCGC
CCAGTTCGCCACCACCGACCCCGAGCCCAGCCTGGATGAGCTGGGCCATCACCTCTACCACAGCAACCCGCCCTTCGACG
TTCGGGGGGCCAACCAGTGGATCAAGTACAAATCCATCAGTTAA

Alignment

ORF - retro_dord_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 99.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLAAVSRVLLGVAQKPATRVLVASRNFANDATFEIKKCDLHRLDEGPPVTTVLTREDGLKYYRMMQTVRR
          MLA.V....LG..QKP..RVL..S.N...DAT..IK.CDL.RL..GP...T.LTR.DGLKYYR.MQ.VRR
Retrocopy MLASVVSRVLGATQKPPLRVLLTSCNYSKDATIDIKSCDLYRLEGGPASSTLLTRDDGLKYYRAMQIVRR

Parental  MELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRRG
          MELKADQLYKQK.IRGFCHLCDGQEACCVG.EA.I.PTD..IT.YRAHG...TRGLSV..ILAELTGRRG
Retrocopy MELKADQLYKQKFIRGFCHLCDGQEACCVGIEAAIKPTDNVITSYRAHGICYTRGLSVKSILAELTGRRG

Parental  GCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGXXXXXXXXXXXXXXXXGQIFEAYNMAAL
          GCAKGKGGSMHMYAK.F.GGNGIVGAQVPLGAGIALACKY.G................GQI.EAYNMAAL
Retrocopy GCAKGKGGSMHMYAKHFFGGNGIVGAQVPLGAGIALACKYLGKRDICLAMYGDGAANQGQIAEAYNMAAL

Parental  WKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATKFAAAYCRSGKGPILME
          WKLPC.FICENNRY.MGT.VERAAASTDYYKRG.FIPGL.V.GMD.LCVREAT.FAA..CR.GKGPI.ME
Retrocopy WKLPCVFICENNRYAMGTAVERAAASTDYYKRGNFIPGLKVNGMDVLCVREATRFAADHCRAGKGPIVME

Parental  LQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFA
          LQTYRYHGHSMSDPGVSYRTREEIQ..RSKSDPIMLL...M....L.SVEELKEIDVEVRKEIE.AAQFA
Retrocopy LQTYRYHGHSMSDPGVSYRTREEIQTMRSKSDPIMLLQEKMISHKLSSVEELKEIDVEVRKEIEEAAQFA

Parental  TADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS
          T.DPEP.L.ELG.H.Y.S.PPF.VRGANQWIK.KS.S
Retrocopy TTDPEPSLDELGHHLYHSNPPFDVRGANQWIKYKSIS

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_35 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 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,