RetrogeneDB ID: retro_ecab_223

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:62560328..62561624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSECAG00000013798
• Aliases: LOC100051840, TUBA1A
• Description: tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]

Sequence

>retro_ecab_223
ATTGGCAATGCCTGCTAGGAGCTCTACTGCCTGGAGCACAGCATCCAGCCCCATGGCCAGATGCCAAGTGACAAGACCAC
TGGGGGAGGAGCTGATTCCTTCCACACCTTCTTCAGTGAGACTAGCGCTGGCAAGCATGTGCCTAGGGCAGTGTTTGTGG
ACCTGGAACCCACAGTCGTCGATGAAGTTCACACTGGCATCTACCGCCAGCTCTTCCGCCATGAGCAGCTCAATACAGGC
AAGGAAGATGCTGCCAATAACTATGCCCATGGGCGCTACACCATTGACAAGGAGATCAGTGACCTCATCTGAGACCAAAT
TTGGAAACTGGCCAACCAGTGCACAGAACTTTAGGGCTTCTTGGTTTTTCACAGCTTTGGTGGGGGAACTGGTTCTGGGT
TCGCCTCTCTGCCGATGGAAGGTCTCTCTGTCGATTATGGCAGGTAGCTCAAGCTGGAGTTCTCCATTTACCCAGCCCCC
CAGGATTCCACAGCTGTAGTTGAGCCCTACAACTCCATCCTCACCACCCGTACCACCACGGCGTACTCTGATTGTGCCTT
CATGTAGACAATGAGGCCATCTATGACATCTGACATAGAAACCTCAATATTGAGTGCCCAATCTATACTAACTTGAATAA
GTTGATAGGTCAAATTGTGTCTTCCATCATTGCTTCCCTCAGATTTGATGAGCCCTGAATGTTGATCTGACAGAATTCCA
GATCAACCTCGTGTGCTCTCCCTGCATCCACTTCCCTCTGGCCACATATGCCCCTGTCATCTCTGTTGAGAAAGCCTACC
ATGAGCAGCTTTCTGTAGCAGAGATCACCAATGCTTGCTTTGAGCCAGCCAACCAGATGGTGAAATGTGATTCATGCGAT
GGTAAATACATGGCTTGTTGCTTGTTGTACTGTGGCAATGTGGTTCCCAAAGATGTCAACACTGCCATTTCCACCATCAA
GACCAAGCGTACCATCTAGTTGTGGATTGGTGCCCCACTGGCTTCAAAGTTGGCATTAATTCCCAGCTTCCCACTGTGGT
ACCTGGTGGAGACCTTGCCAAAGGGCAGCAAGCTGTGTGCACACTGAGCAATACCACAGCCACTGCTGAGGCCTGGGCTG
GCCTGGACCGCAAGTTTGACCTGATGTATGCCAAGCGTGCCTTTGTTCACTGGTATGTGAACATGGAGGGCATGAAGGAA
GGAGAGTTTTCTGAAGCCCATGAGGACACGGCTGCCCTTGAGAAGGGTTATGAGAAGGTTGGTGTGGATTCTGTTGACAG
AGAGGGTGAGGAAGAA

Alignment

ORF - retro_ecab_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.34 %
• Parental protein coverage: 95.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQ
          IGNAC.ELYCLEH.IQP.GQMPSDKT.GGG.DSF.TFFSET.AGKHVPRAVFVDLEPTV.DEV.TG.YRQ
Retrocopy IGNAC*ELYCLEHSIQPHGQMPSDKTTGGGADSFHTFFSETSAGKHVPRAVFVDLEPTVVDEVHTGIYRQ

Parental  LFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLME
          LF..EQL.TGKEDAANNYA.G.YTI.KEI.DL..D.I.KLA.QCT.L.GFLVFHSFGGGTGSGF.SL.ME
Retrocopy LFRHEQLNTGKEDAANNYAHGRYTIDKEISDLI*DQIWKLANQCTEL*GFLVFHSFGGGTGSGFASLPME

Parental  RLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFM-VDNEAIYDICRRNLDIERPTY
          .LSVDYG...KLEFSIYPAPQ.STAVVEPYNSILTT.TT...SDCAFM.VDNEAIYDI..RNL.IE.P.Y
Retrocopy GLSVDYGR*LKLEFSIYPAPQDSTAVVEPYNSILTTRTTTAYSDCAFM<VDNEAIYDI*HRNLNIECPIY

Parental  TNLNRLIGQIVSSITASLRFDG-ALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITN
          TNLN.LIGQIVSSI.ASLRFD..ALNVDLTEFQ.NLV..P.IHFPLATYAPVIS.EKAYHEQLSVAEITN
Retrocopy TNLNKLIGQIVSSIIASLRFDE<ALNVDLTEFQINLVCSPCIHFPLATYAPVISVEKAYHEQLSVAEITN

Parental  ACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTI-QFVDWCPTGFKVGINYQPPTV
          ACFEPANQMVKCD...GKYMACCLLY.G.VVPKDVN.AI.TIKTKRTI...VDWCPTGFKVGIN.Q.PTV
Retrocopy ACFEPANQMVKCDSCDGKYMACCLLYCGNVVPKDVNTAISTIKTKRTI<LVVDWCPTGFKVGINSQLPTV

Parental  VPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVG-EGMEEGEFSEAREDMAALEKD
          VPGGDLAK.Q.AVC.LSNTTA.AEAWA.LD.KFDLMYAKRAFVHWYV..EGM.EGEFSEA.ED.AALEK.
Retrocopy VPGGDLAKGQQAVCTLSNTTATAEAWAGLDRKFDLMYAKRAFVHWYVNMEGMKEGEFSEAHEDTAALEKG

Parental  YEEVGVDSVEGEGEEE
          YE.VGVDSV..EGEEE
Retrocopy YEKVGVDSVDREGEEE

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	0.00 RPM
SRP021940_cerebellum	0.52 RPM	0.05 RPM
SRP021940_embryo	2.02 RPM	279.10 RPM
SRP021940_placental_villous	0.38 RPM	53.16 RPM
SRP021940_synovial_membrane	0.41 RPM	44.75 RPM
SRP021940_testis	0.13 RPM	26.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_223 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223 ,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Equus caballus	ENSECAG00000014631	1 retrocopy	retro_ecab_147,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,