RetrogeneDB ID: retro_ecab_21

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:42997462..42998629(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001158
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSECAG00000001964
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_ecab_21
ATGCTCGCTGCCGCCGTCTCCCGCGTGTTGGGAGGAGGGGCCCAGAAGCCCGCTAGCAGAGTGCTGGTGGCGTCCTGTAA
CTATTCAAATGATGCCACATTTGAAATTAAGAAATGTGATCTTCATCGGTTGGAAGAGGGTCCGCCTGTCACAGCAGTGC
TCACCCGGGAGGATGGGCTCCAGTACTACAGGATGATGCAGACTGTTCGCCGAATGGAATTGAAGGCAGATCAGCTGTAT
AAACAGAAATTTATTCGTGGTTTCTGCCACTTGTGTGATGGTCAGGAAGCTTGTTATGTGGGCCTTAAGGCCGGGGCAAA
TCCCTCCGATCACGCGATCACAGCCTATCGGGCTCACGGCTTATGCTACGCTTACGGACTTTCTGTGCAATCAATTCTTG
CAGAGCTGACTGGACGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGATCGATGCATATGTACGGCAGGAACTTCTATGGG
GGCAACGGCATTGTTGGTGCTCAGGTACCCCTGGGAGCTGGTGTTGCTCTGGCCTGTAAATATAAGGGAAGCAATGAGGT
CTGTTTGACTCTGTATGGGGATGGTGCTGCTAATCAGGGTCAGATATTTGAAGCTTATAATATGGCAGCTTTGTGGAAAT
TACCTTGTATTTTCATCTGTGAGAATAATCGCTATGGAATGGGAACAGCTATTGAGAGAGCATCAGCCAGCACTGACTAC
TACAAGAGAGTTAATTTTATCCCTGGACTAAGGGTAGATGGAATGGATGTCCTATGTGTTCGAGAGGCAGCTAAGTTTGC
AGCTGACTACTGTAGATCTGGAAAGGGACCCATAGTGATGGAGCTGCAGACATACCGTTATCATGGGCATAGTATGAGTG
ATCCTGGAATCAGTTATCGTACCAGAGAGGAAATTCAGAACATAAGAAGTAAGAGTGATCCCATTATGCTTCTCAAAGAT
AAAATGTTGAACAACAAGCTTTCCAGTATTGAAGAATTGAAAGAAATTGATGTTGGAGTGAGGAAAGAAATTGATGATGC
AGCCCAGTTTGCTACAACTGATCCAGAGCCACCACTGGAAGAATTAGGCCATCATGTCTACAACAATAATCTACCTTTTG
AAGTTCGTGGTACAAATCAGTGGATCAAGTTTAAGTCCATCAGTTAA

Alignment

ORF - retro_ecab_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 99.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLAAVSRVLSGVAQKPASRVLVASRSFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLRYYRMMQTVRR
          ..AAVSRVL.G.AQKPASRVLVAS....NDATFEIKKCDLHRLEEGPPVT.VLTREDGL.YYRMMQTVRR
Retrocopy LAAAVSRVLGGGAQKPASRVLVASCNYSNDATFEIKKCDLHRLEEGPPVTAVLTREDGLQYYRMMQTVRR

Parental  MELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRRG
          MELKADQLYKQK.IRGFCHLCDGQEAC.VGL.AG.NP.DH.ITAYRAHG.....GLSV..ILAELTGRRG
Retrocopy MELKADQLYKQKFIRGFCHLCDGQEACYVGLKAGANPSDHAITAYRAHGLCYAYGLSVQSILAELTGRRG

Parental  GCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYFGKDEVCLTLYGDGAANQGQIFEAYNMAAL
          GCAKGKGGSMHMY..NFYGGNGIVGAQVPLGAG.ALACKY.G..EVCLTLYGDGAANQGQIFEAYNMAAL
Retrocopy GCAKGKGGSMHMYGRNFYGGNGIVGAQVPLGAGVALACKYKGSNEVCLTLYGDGAANQGQIFEAYNMAAL

Parental  WKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILME
          WKLPCIFICENNRYGMGT..ERA.ASTDYYKR..FIPGLRVDGMD.LCVREA..FAA.YCRSGKGPI.ME
Retrocopy WKLPCIFICENNRYGMGTAIERASASTDYYKRVNFIPGLRVDGMDVLCVREAAKFAADYCRSGKGPIVME

Parental  LQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFA
          LQTYRYHGHSMSDPG.SYRTREEIQ..RSKSDPIMLLKD.M.N..L.S.EELKEIDV.VRKEI.DAAQFA
Retrocopy LQTYRYHGHSMSDPGISYRTREEIQNIRSKSDPIMLLKDKMLNNKLSSIEELKEIDVGVRKEIDDAAQFA

Parental  TADPEPPLEELGHHIYSSDPPFEVRGANQWIKFKSIS
          T.DPEPPLEELGHH.Y....PFEVRG.NQWIKFKSIS
Retrocopy TTDPEPPLEELGHHVYNNNLPFEVRGTNQWIKFKSIS

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
SRP021940_articular_cartilage	0.00 RPM	14.23 RPM
SRP021940_cerebellum	0.00 RPM	69.59 RPM
SRP021940_embryo	0.00 RPM	51.35 RPM
SRP021940_placental_villous	0.10 RPM	31.27 RPM
SRP021940_synovial_membrane	0.00 RPM	29.02 RPM
SRP021940_testis	87.60 RPM	15.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_21 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_21 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
Bos taurus	retro_btau_100

---

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,