RetrogeneDB ID: retro_ecab_1041

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0076:114329..115230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSECAG00000009504
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_ecab_1041
ATGCATGAACGCACGTTCATTCACCTTGGCCAGGCCAGTGTCCAGATTGGCAATGCCTGCTTGAAGTTCTATTGCCTGAA
AAATGGCATCCAGCCCAATGGCCAGATGCTAAGTGACAAGATCATTGGGGCAGGAGATGACTCCTTCAACAGCTTCCTCA
GTGGGACAGCTGCTGGCAAGCATGTGTGCAGGGTCATGTTTGTAGACCTGAAATCCACAGTCATTGATGAAGTTCACACT
GGAACTTACCACCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTAACAATAACTATGCCTTCAGGTA
CAACCATTGGTAAGATCATTGCCCTCCTCATGTACTGAATTCATAAGCTGAGAACCAATGCAGAAGTTTTCAGGGCCTCT
AGGTTTTCCACAGCTTTGCAGGGCAACTGGTTCTTAGTCCACCTCCCTACAGGTGGCACTTTTCTCTGTAGGTGATGCCA
AGATGTCCAAACTGCAGTTCTCCATTTACCCAGCACCCCCAGGTTTCCACAGCTGTTGTTGAAGCCCACGACTCCATTCT
CACCACCCATACCACCCTGGAGCACTCCGATTGTGCCTCTGTTGTAGAAAATGAGGCCATCTATGACCTCTATTATAGAA
ACCTCAATATTGAGCACCCAACCTACACTAACCTTAACCACCTTATTAGTCAGACTGTGTCCTCCATCACTAACTGCTTA
TTTCAGATTTGATGGAGCCCTGAATATTCATCTGACAGAATTCCAGGCCATCCTGATGCCCTATTCCTGCATCCACCTCC
CTCTGGTCACATATGCCCTTGTCATCTCTTCTAAGAAAGCTTACCATGAACATCTTACTGTAGCAGAGATCAACAAGGTA
TACTTTGAGCCAGTCAACAAG

Alignment

ORF - retro_ecab_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.82 %
• Parental protein coverage: 67.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          M.E...IH.GQA.VQIGNAC...YCL..GIQP.GQM.SDK.IG.GDDSFN.F.S.T.AGKHV.R..FVDL
Retrocopy MHERTFIHLGQASVQIGNACLKFYCLKNGIQPNGQMLSDKIIGAGDDSFNSFLSGTAAGKHVCRVMFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHY-TIGKEIIDLVLDRIRKLA-DQCTGLQGFLVF
          ..TVIDEV.TGTY.QLFHPEQLITGKEDA.NN.....Y.TIGK.II.L....I.KL...QC...QG..VF
Retrocopy KSTVIDEVHTGTYHQLFHPEQLITGKEDA-NNNYAFRY>TIGK-IIALLMY*IHKLR<NQCRSFQGL*VF

Parental  HSFGG-GTGSGFTSLLMERLSVDYGKKSKLEFSIYPAP-QVSTAVVEPYNSILTTHTTLEHSDCAFMVDN
          HSF.G..TGS..TSL.....SV...K.SKL.FSIYPAP.QVSTAVVE...SILTTHTTLEHSDCA..V.N
Retrocopy HSFAG<ATGS*STSLQVALFSVGDAKMSKLQFSIYPAP>QVSTAVVEAHDSILTTHTTLEHSDCASVVEN

Parental  EAIYDICRRNLDIERPTYTN-LNRLISQIVS-SITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAP
          EAIYD...RNL.IE.PTYTN.L..L.......S.TA..RFDGALN..LTEFQ..L.PY..IH.PL.TYA.
Retrocopy EAIYDLYYRNLNIEHPTYTN>LTTLLVRLCPPSLTAYFRFDGALNIHLTEFQAILMPYSCIHLPLVTYAL

Parental  VISAEKAYHEQLTVAEITNACFDPTNQ
          VIS..KAYHE.LTVAEI....F.P.N.
Retrocopy VISSKKAYHEHLTVAEINKVYFEPVNK

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	0.00 RPM	0.00 RPM
SRP021940_embryo	0.15 RPM	148.86 RPM
SRP021940_placental_villous	0.00 RPM	105.99 RPM
SRP021940_synovial_membrane	0.05 RPM	49.52 RPM
SRP021940_testis	0.00 RPM	31.46 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1041 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
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,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,