RetrogeneDB ID: retro_ecab_147

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:136437928..136439224(+)
• Located in intron of: ENSECAG00000022427

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBAL3
• Ensembl ID: ENSECAG00000014631
• Aliases: None
• Description: tubulin, alpha-like 3 [Source:HGNC Symbol;Acc:23534]

Sequence

>retro_ecab_147
AAGTGCACCTCCATCCAGTTTGGCCAGGCTGGTATCCAGATGGGCAATGCCTGCTGGGAGCTCTACTGCCAGGAACATGG
CATCCAGTCCAACGGCCAGATGCCAAGGGACAAGACCATTAGGGGAAGAGATAACTCCCTCAACACATTCTTCAGTGACA
CAGGCATTGACAAGTATGTGCCCAGAGCAGTGTTTGTAGACCTGGAACCCATGGTCATTGATGAAGTTTGCACTGGCACC
TACCATCAGCTCTTTCACCCTGAACAGCTCATCAGAGGCAAGGAAGATGCTGTCAATAACTATGCCCATGGGCACTACAC
CATTGGTAAGGTGATCATTGACCTTGTCTTGGACCAAATTTGGAAACTGGCCAGCCAGTGTATGGGTCTTCAGAGCTTCT
TGGTTTTCAACAGCTTTGGTGGGGGAACTGGTTCTGGGCTCACCTCTCTGTTGATGGAATGTCTCTGTCAACTATGGCAA
GAAGTCCAAGCTGGAGTTCTCCATTTACCAAGCCCCCAGGTTTCCACAGGTATAGTTGAGTGCCACAACTCCATCCTCAC
CACTTACACCACCCTGGAGCACTGTGATTGTGCCTTTATGGTAGACAAGGAGGCCATCTATGACATCTGTTGTAGAAGCC
TCACTATTGAGTGTCTAACCTATACTAACCTGAATAGGTTGATAGGTCAAATTGTGTCCTGCATCGCTGCTTCCCTCAGA
TTTGATGTAGCTCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTCCCTCTTGC
CCTGTATGCCCCTGTCATCTTTGTTGAGAAAGCCTACCATGAATAGCTTTCTGTAGCAGAGATCAGAACGCTTCTTTTGA
GCCAGCCAACCAGATGGTGAAATGTGATCCTTGCCATGGTAAATACACGGCTTGTTGCCTGTTGTACCATGGTGATGTGG
TTCCCAAAGATGTCAATGCTGCTGTTGCCATCATCAAGACCAAGCATACCATCCAGTTTGTAGATTGGTGCCCCACTGGC
TTCAAAGTTGGCATCAATCACCAGCTTCCCACTGTGGTATCTGGTGGAGACCTGGCCAAACTACAGTGAAGTGTGTGCAT
GCTGAGCAATACCACAGCCATTGCTGAGGCCTGGGCTAGCCTGGACCACAGCTTGACCTGATGATGCCAAGCGTGTCTTT
ATTCATTGGTACGTGGGTGAGCGCATGGAAGAAGGAGAGTGTTCTGAGGGCTGTGAGGACATGGCTGCCCCTTAGAAGGA
TTACTAGGAGGTTGGT

Alignment

ORF - retro_ecab_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.41 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ECLSIHIGQAGIQIGDACWELYCLEHGIQPDGGL-ENANVEHMDASFDTFFCETRAGKYVPRALFMDLEP
          .C.SI..GQAGIQ.G.ACWELYC.EHGIQ..G...........D.S..TFF..T...KYVPRA.F.DLEP
Retrocopy KCTSIQFGQAGIQMGNACWELYCQEHGIQSNGQMPRDKTIRGRDNSLNTFFSDTGIDKYVPRAVFVDLEP

Parental  TVVDGIRTGKYRSLFHPEQLVSGKEDAANNYARGHYSVGSEIIDLVLERIRKLAKQCSGLQGFLIFRSFG
          .V.D...TG.Y..LFHPEQL..GKEDA.NNYA.GHY..G..IIDLVL..I.KLA.QC.GLQ.FL.F.SF.
Retrocopy MVIDEVCTGTYHQLFHPEQLIRGKEDAVNNYAHGHYTIGKVIIDLVLDQIWKLASQCMGLQSFLVFNSF-

Parental  GGTGSGFTSLLMEQ-LSIEYSRKTKLEFSVY-PAPRISTAVVEPYNSILTTHSTIEHSDCSFMVDNEAIF
          GG........L.....S..Y..K.KLEFS.Y.P.P..ST..VE..NSILTT..T.EH.DC.FMVD.EAI.
Retrocopy GGGTGSGLTSLLME>VSVNYGKKSKLEFSIY<PSPQVSTGIVECHNSILTTYTTLEHCDCAFMVDKEAIY

Parental  DICHRKLGVERPSYASINRLIGQAVSSITASLRFKGPLNVDLIEFQTNLVPYPRIHFPMTTFAPIISADK
          DIC.R.L..E...Y...NRLIGQ.VS.I.ASLRF...LNVDL.EFQTNLVPYPRIHFP....AP.I...K
Retrocopy DICCRSLTIECLTYTNLNRLIGQIVSCIAASLRFDVALNVDLTEFQTNLVPYPRIHFPLALYAPVIFVEK

Parental  AYHEELSVSDITA-ACFEFSNQLVKCDPRLGKYMACCLLYRGDVVPKDVNAAIAAMKSRNSVRFVDWCPT
          AYHE.LSV..I...A.FE..NQ.VKCDP..GKY.ACCLLY.GDVVPKDVNAA.A..K......FVDWCPT
Retrocopy AYHE*LSVAEIRT<ASFEPANQMVKCDPCHGKYTACCLLYHGDVVPKDVNAAVAIIKTKHTIQFVDWCPT

Parental  GFKVGINNQPPVAMPGGDLAKVQRAVCMLSNTTAIVEAWARLDH-KFDLMY-AKRAFLHWYIREGMEEGE
          GFKVGIN.Q.P....GGDLAK.Q..VCMLSNTTAI.EAWA.LDH...DLM..AKR.F.HWY..E.MEEGE
Retrocopy GFKVGINHQLPTVVSGGDLAKLQ*SVCMLSNTTAIAEAWASLDH<QLDLMM<AKRVFIHWYVGERMEEGE

Parental  FSEAREDLAALEKDYEEVG
          .SE..ED.AA..KDY.EVG
Retrocopy CSEGCEDMAAP*KDY*EVG

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	0.12 RPM	0.00 RPM
SRP021940_cerebellum	0.16 RPM	0.10 RPM
SRP021940_embryo	0.82 RPM	0.26 RPM
SRP021940_placental_villous	0.05 RPM	0.05 RPM
SRP021940_synovial_membrane	0.14 RPM	0.08 RPM
SRP021940_testis	0.06 RPM	0.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_147 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_147 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124,
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 ,