RetrogeneDB ID: retro_ecab_1030

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:59412366..59412672(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015686
• Aliases: None
• Description: None

Sequence

>retro_ecab_1030
ATGCCCCATCAAGGGGAGAATGTTAATAAAGAGACAGATTTTATAAGATAGAACCAAGTGAAGATGCTGGAATTGTAAAT
TGCAGTAACTGAAATGACAATTCACTAGAGGGACTCAACAGTAGATCTGTCTGAACTAGCAAAAGAAAGAAAGAGCAAAC
TTGAAGATCGATCAAAGGAGATTATGCAGTCCAAACAAGAAGGAGAAAACAGAATGGAGAGAAACAGTCTCAGAGAAATG
AGGGACACAATTAAGAGTACCAACATATGTGTAATGGGAGTACCAGAAGGAGAGGGGAGAGAGAAA

Alignment

ORF - retro_ecab_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.89 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDEHSGNFNKETDSIRKCQIEVTELKNTIPELT-NTLEGFNSR-LDE-AEERISELNDRA-ELTQSEQQK
          M.....N.NKETD.IR..Q....EL.....E.T.N.LEG.NSR.L.E.A.ER.S.L.DR..E..QS.Q..
Retrocopy MPHQGENVNKETDFIR*NQVKMLEL*IAVTEMT<NSLEGLNSR>LSELAKERKSKLEDRSKEIMQSKQEG

Parental  EKRMKNTDNSLRELWDNIKHANIRIIGVPEGEERDK
          E.RM....NSLRE..D.IK..NI...GVPEGE.R.K
Retrocopy ENRMER--NSLREMRDTIKSTNICVMGVPEGEGREK

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	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1030 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1030 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015686	14 retrocopies	retro_ecab_1030 , retro_ecab_1031, retro_ecab_1111, retro_ecab_1127, retro_ecab_207, retro_ecab_208, retro_ecab_326, retro_ecab_487, retro_ecab_491, retro_ecab_518, retro_ecab_607, retro_ecab_625, retro_ecab_863, retro_ecab_881,