RetrogeneDB ID: retro_btau_100

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:30063544..30064720(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000026250
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSBTAG00000019852
• Aliases: PDHA1, PDHA
• Description: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:A7MB35]

Sequence

>retro_btau_100
ATGAAGAAGATGCTGACTGCTGCTGTCTCTCGCGTGCTGTCTGGTGTCACCCAGAAGCCCGCTAGCAGAGTGCTTGTTGC
CTCCTGTAAATATTCAAACAATGCTACCTTTGAGATTAAGAAATGTGATCTTTATCGGTTGGAAGAGGGTCCCCCTGTCA
CTACCGTGCTCACCCGGGAGGATGGACTCAAATACTACAAGATGATGCAGACTATTCGTCGAATGGAACTGAAGGCAGAT
CAGTTGTATAAACAGAAATTTATTCGTGGTTTCTGTCACTTGTGTGATGGTCAGGAAGCTTGTTGTGTGGGTCTTGAGGC
TGGGATAAATCCCACGGATCATGTCATTACGTCCTATCGGGCTCACGGCTTAAGTTATACGCGGGGACTTACTGTCCGAT
CAATTCTTGCAGAGCTGACCGGACGAAGAGCTGGTTGTGCTAAAGGAAAAGGAGGGTCCATGCATATGTATGCCAAGAAC
TTCTATGGGGGCAACGGCATTGTCGGCGCTCAGGGACCACTGGGAGCTGGTGTTGCTTTGGCCTGTAAATACAAGGGGAA
CAACGAGGTGTGTTTGACTCTGTATGGCGATGGCGCAGCTAATCAGGGTCAGATATCTGAAGCTTACAATATGGCGGCTT
TGTGGAATTTACCTTGCATTTTCATCTGTGAGAATAACCGCTATGGAATGGGAACATCTGTGGACAGAGCTGCAGCCAGC
ACTGATTACTACAAGAGAGGCAATTTTATCCCTGGACTAAGAGTAGATGGAATGGATATTCTATGTGTTCGGGAGGCAAC
TAAGTTTGCAGCTGACTATTGTAGATCTGGAAAGGGACCCATACTGATGGAGCTGCTGACATACCGTTATCATGGACACA
GTATGAGTGATCCTGGAATCAGTTACCGTACACGAGAAGAAATTCAGAGTGTAAGAAGTAAGAGTGATCCTATCATGCTT
CTCAAAGATAAAATGGTAAACAACCAGCTTGCCAGTGTTGAAGAATTGAAGGAAATTGATGTTGAAGTGAGGAAAGAAAT
TGATGATGCAGCTCAGTTTGCTATGACTGATCCAGAACCACCTTTGGAAGAATTAGGCCATCACATCTACAGCAGTAATC
CACCTTTTGATATTCGTGGTGCAAATCAGTGGATCAAGTTTCAGTCAGTCAGTTAA

Alignment

ORF - retro_btau_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRKML-AAVSRVLSGVAQKPASRVLVASRHFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQ
          M.KML.AAVSRVLSGV.QKPASRVLVAS....N.ATFEIKKCDL.RLEEGPPVTTVLTREDGLKYY.MMQ
Retrocopy MKKMLTAAVSRVLSGVTQKPASRVLVASCKYSNNATFEIKKCDLYRLEEGPPVTTVLTREDGLKYYKMMQ

Parental  TVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELT
          T.RRMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGINPTDH.IT.YRAHG...TRGL.VR.ILAELT
Retrocopy TIRRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPTDHVITSYRAHGLSYTRGLTVRSILAELT

Parental  GRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYN
          GRR.GCAKGKGGSMHMYAKNFYGGNGIVGAQ.PLGAG.ALACKY.G..EVCLTLYGDGAANQGQI.EAYN
Retrocopy GRRAGCAKGKGGSMHMYAKNFYGGNGIVGAQGPLGAGVALACKYKGNNEVCLTLYGDGAANQGQISEAYN

Parental  MAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATKFAAAYCRSGKGP
          MAALW.LPCIFICENNRYGMGTSV.RAAASTDYYKRG.FIPGLRVDGMDILCVREATKFAA.YCRSGKGP
Retrocopy MAALWNLPCIFICENNRYGMGTSVDRAAASTDYYKRGNFIPGLRVDGMDILCVREATKFAADYCRSGKGP

Parental  ILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDA
          ILMEL.TYRYHGHSMSDPG.SYRTREEIQ.VRSKSDPIMLLKD.MVN..LASVEELKEIDVEVRKEI.DA
Retrocopy ILMELLTYRYHGHSMSDPGISYRTREEIQSVRSKSDPIMLLKDKMVNNQLASVEELKEIDVEVRKEIDDA

Parental  AQFATADPEPPLEELGYHIYCNDPPFEVRGANQWIKFKSIS
          AQFA..DPEPPLEELG.HIY...PPF..RGANQWIKF.S.S
Retrocopy AQFAMTDPEPPLEELGHHIYSSNPPFDIRGANQWIKFQSVS

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	84.78 RPM
ERP005899_muscle	0.00 RPM	102.99 RPM
SRP017611_brain	0.00 RPM	93.09 RPM
SRP017611_kidney	0.12 RPM	269.86 RPM
SRP017611_liver	0.00 RPM	71.66 RPM
SRP030211_testis	177.87 RPM	9.36 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_100 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_100 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_41
Pan troglodytes	retro_ptro_79
Gorilla gorilla	retro_ggor_59
Pongo abelii	retro_pabe_129
Macaca mulatta	retro_mmul_123
Callithrix jacchus	retro_cjac_27
Mus musculus	retro_mmus_63
Oryctolagus cuniculus	retro_ocun_264
Equus caballus	retro_ecab_21

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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,