RetrogeneDB ID: retro_ecab_1127

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:99988101..99988544(-)
• 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_1127
ATGAAGAAACAAAGGAATATGTTGCAAAAGAAAGAACAAAATAAAACTCCAGAAACAGACCTTAATGAAACAAAGATAAG
TGATTTACCTGATAATGAGCTCAAGATAATGGTTATAAAGATGCTCACTGAGGTCAGGAGAAAAATGCATGAGCAAAGTG
AGCATTTCAACAAAGGTACAGAAAATATAAGAAAGTACCAAACAGAAGTCACAAAGCTGAAGAATACAATAACTGTACTG
AAAAGTTCAACAGAGGAGTTCAACAACAGGGTAGATCAAGCAGAAGTAAGGATCAGTCAACTGAAAGGGCAGTAGAATAC
ACCCACTCAGAGGAGCAAAAAGAAAAAAGAATGAAAAAGAGCAAAAATAGCTTAAAGGACTTACAGGAGATCATCAAGTG
GACCAATAGTCAAATTATAGGGGTCTCAGAAGGAAAAGAAAGA

Alignment

ORF - retro_ecab_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.01 %
• Parental protein coverage: 86.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKKQGNMFQMKEQDK-PENNLNEMEVSNLPNKEFQVKVIKMLTKLKRRMDEHSGNFNKETDSIRKCQIEV
          MKKQ.NM.Q.KEQ.K.PE..LNE...S.LP..E....VIKMLT...R.M.E.S..FNK.T..IRK.Q.EV
Retrocopy MKKQRNMLQKKEQNKTPETDLNETKISDLPDNELKIMVIKMLTEVRRKMHEQSEHFNKGTENIRKYQTEV

Parental  TELKNTIPELTNTLEGFNSRLDEAEERISELNDR-AELTQSEQQKEKRMKNTDNSLRELWDNIKHANIRI
          T.LKNTI..L....E.FN.R.D.AE.RIS.L.....E.T.SE............SL..L...IK..N..I
Retrocopy TKLKNTITVLKSSTEEFNNRVDQAEVRISQLKGQ<VEYTHSEEXXXXXXXXXXXSLKDLQEIIKWTNSQI

Parental  IGVPEGEER
          IGV.EG.ER
Retrocopy IGVSEGKER

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_1127 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1127 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,