RetrogeneDB ID: retro_ecab_671

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:8650047..8650811(+)
• Located in intron of: ENSECAG00000026836

Retrocopy information

• Ensembl ID: ENSECAG00000011490
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000006639
• Aliases: None
• Description: None

Sequence

>retro_ecab_671
AATATAGAGAAACAATTCAATGAGTTCAGGAGCTACTTCACAAAAGACATTGAAACTATAAAGAAGAATGAATCAGAAAT
ACTAGAGATGAAAAATACAATGGATCAGATAAAACAAAATATGGATTCCCTGAATGTATGTGTGGACACCATAGAGGAGC
AAATCAGCATAATTGAAGATAGACAGGTTGAATGGCTCCAGACAGAGGGAGAGAGAGAACTAAGACTAAAAAGAAATGAA
TAAAACCTCTGAGAAATAGCTGACTCAATGAGGAAATGCAACATAAGAATTATAGGTATCCCCGAAGAGGAAGAAAAGGA
GAATGGAGCAGAAAGCGTGCTCAAAGAAATAATAGCAGAGAACTTCCCAAATCTAGGGAATGAGAGAGAAATGTGTGTGG
AGGAAGCTTTCAGATCTCCTAGATATATCAATGTAAAGACCTACTGCAAGGCATACAGTAGTAAACCTGGCAAAAATGAA
TGACAAAGAAAGAATACTCAGGGCAGCAAGGTAGCAGAAAATAACCTATAAAGGAACACCTATCAGACTTTCAGCAGATT
TCTCTGCAGAAACCTTACAAGATGGAGAGATTGGAATGACATATTCAAAACTTTAAAAGATAAAAATCTTCAGCAAAACT
ACTCTATCCAGCAAAAATATCCTTCAGATATGAGGGAGAAATTAAATCCTTCCCAGACAAATACAAGCTAAGGGACTTCG
TAGCCACGAGACCACCACTACAAAAAATCCTCAAGAAGGCCCTC

Alignment

ORF - retro_ecab_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.77 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLGRRMGELSENINKEVGNIKKNQS---EMKNTILERKISLEGLNSRVDDTEEWMSKLDKRQEEITQAEQ
          .......E......K....IKKN.S...EMKNT....K.....LN..VD..EE..S....RQ.E..Q.E.
Retrocopy NIEKQFNEFRSYFTKDIETIKKNESEILEMKNTMDQIKQNMDSLNVCVDTIEEQISIIEDRQVEWLQTEG

Parental  IKEKKIQKEGENFQETTDSMRKCNIRIIRIPEGDEKENGTESVLKGIIAENFPDLENETETRVEEAFRSP
          ..E........N..E..DSMRKCNIRII.IPE..EKENG.ESVLK.IIAENFP.L.NE.E..VEEAFRSP
Retrocopy ERELRLKRNE*NL*EIADSMRKCNIRIIGIPEEEEKENGAESVLKEIIAENFPNLGNEREMCVEEAFRSP

Parental  RYVNVKR-TTARHIVVKLAKLND-ERILRAARQKKITYKGTPLRLSVDFSVETLQ-AWRDWNDILKTLKD
          RY.NVK..T.....V..LAK.ND.ERILRAAR..KITYKGTP.RLS.DFS.ETLQ..WRDWNDI.KTLKD
Retrocopy RYINVKT>TARHTVV-NLAKMNDKERILRAAR*QKITYKGTPIRLSADFSAETLQ<RWRDWNDIFKTLKD

Parental  NNLQ-PRILYPAKISFRYEGE-KSFLDKQKLRDFTAMRPPAPQEILKKAL
          .NLQ....LYPAKISFRYEGE.KSF.DK.KLRDF.A.RPP..Q.ILKKAL
Retrocopy KNLQ<AKLLYPAKISFRYEGEIKSFPDKYKLRDFVATRPPL-QKILKKAL

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	0.03 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.05 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_671 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_671 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005242	2 retrocopies	retro_ecab_192, retro_ecab_934,
Equus caballus	ENSECAG00000006639	4 retrocopies	retro_ecab_274, retro_ecab_484, retro_ecab_671 , retro_ecab_689,