RetrogeneDB ID: retro_ecab_274

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 12:9018995..9019693(-)
• Located in intron of: ENSECAG00000015881

Retrocopy information

• Ensembl ID: ENSECAG00000019883
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ecab_274
AGTTCTGGAGTTACTTCACAAGAGACTGAAACTTTAAAGAACCAATCAGAAATACTAGAGATGAAAAACACAATGGACCA
GATAAAACAGAATATGGATTCCCTGAATGCCCGTGTGGACGCCATAGAGGAGCAAATCAGCATAACTGAAGATAGGTTGA
ACGGCTCCAGACAGAGGAAGAGAGAGACTAAAGGACTAAAAAGGAATGAAGAAAATCTCCGAGAAATAGCCAACTTAACG
AGCAAATGCAAAGTAAGAATAAGTGGAATCCCTGAGGGTGACGAAAAGGAGAATGGAACAGAAAGCGTGGTCAAAGAAAT
AGTAGCAGAGAACTTCCCAAATCTAGGGAATGAGAGAGAAAGGTGGGTGGAGGAAGCTTTCAGGTCTCCTACATATGTCA
ATGTAAAAAGACCTACTGCAAGGCATATAGTAGTAAAACTGGCAAAAGTGAATGACAAAGAAAGAATACTTAGGGCAGCA
AGGCAGAAGAAAATAACAAAGGAACCACTGTCAGACTTTCAGAGGATTTCTCTGCAGAAACCTTACAAGCCAGGGGAGAA
TGGAATGACATATTCAAAACTTCAAAAGATAACAATCTTCAGCCAAGAATACTCTATCCAGCAAAAATATCCTTCAGATA
TGGAGAAATGAAACCTTCCCCAAAAAAACAAAAGCTAACGGACTTTGTAGCCATGAGA

Alignment

ORF - retro_ecab_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.17 %
• Parental protein coverage: 90.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SENINKEVGNIKKNQS---EMKNTILERKISLEGLNSRVDDTEEWMSKLDKRQEEITQAEQIKEKKIQKE
          S...........KNQS...EMKNT....K.....LN.RVD..EE..S....R.....Q......K.....
Retrocopy SSGVTSQETETLKNQSEILEMKNTMDQIKQNMDSLNARVDAIEEQISITEDRLNGSRQRKR-ETKGLKRN

Parental  GENFQETTDSMRKCNIRIIRIPEGDEKENGTESVLKGIIAENFPDLENETETRVEEAFRSPRYVNVKRTT
          .EN..E......KC..RI..IPEGDEKENGTESV.K.I.AENFP.L.NE.E..VEEAFRSP.YVNVKR.T
Retrocopy EENLREIANLTSKCKVRISGIPEGDEKENGTESVVKEIVAENFPNLGNERERWVEEAFRSPTYVNVKRPT

Parental  ARHIVVKLAKLNDERILRAARQKKI-TYKGTPLRLSVDFSVETLQAWRDWNDILKTLKDNNLQPRILYPA
          ARHIVVKLAK.ND......A...K....KGT..RLS.DFS.ETLQA...WNDI.KT.KDNNLQPRILYPA
Retrocopy ARHIVVKLAKVNDKERILRAARQKK<NNKGTTVRLSEDFSAETLQARGEWNDIFKTSKDNNLQPRILYPA

Parental  KISFRYEGEKSFLDKQKLRDFTAMR
          KISFRY...K....KQKL.DF.AMR
Retrocopy KISFRYGEMKPSPKKQKLTDFVAMR

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	0.03 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_274 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_274 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,