RetrogeneDB ID: retro_ecab_416

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:37938713..37939117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRABP1
• Ensembl ID: ENSECAG00000015978
• Aliases: None
• Description: cellular retinoic acid binding protein 1 [Source:HGNC Symbol;Acc:2338]

Sequence

>retro_ecab_416
CCCAACTTCGCGGACACCTGGAAGCTGATCAGCAGTGAGAATTTTGACGAGCTACTCAAGACGCCGGGCGTGAACGCCAT
GCTGAGGAAAGTGGCCGTGGTGACTGAGTCCAAGCCGCACGTGGAGATCCGCCAGGATGATCAGTTCTGTATCAAGACAT
CCACCACGGTGTGCACCACCAAGATCAACTTCAAGGTCGGAGAAGGCTTTGATGAGGAGACAGTGGATGGACGCAAGTGC
AGGAGTTTAGCCACTTGAGAGAATGAAAACAAGATCCACTGCACACAAACTCTCATTGAGGGGGAGGCCCCAAAACCTAC
TGCACCTGCGAGCTGGCCAGTGACGAGCTCATCATGAAGTTCGGCGCCCACGACTTGGTCTGCACGAGAATTTATGTTCG
GAAG

Alignment

ORF - retro_ecab_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNFAGTWKMRSSENFDELLKALGVNAMLRKVAVAAASKPHVEIRQDGDQFYIKTSTTVRTTEINFKVGEG
          PNFA.TWK..SSENFDELLK..GVNAMLRKVAV...SKPHVEIRQD.DQF.IKTSTTV.TT.INFKVGEG
Retrocopy PNFADTWKLISSENFDELLKTPGVNAMLRKVAVVTESKPHVEIRQD-DQFCIKTSTTVCTTKINFKVGEG

Parental  FEEETVDGRKCRSLATWENENKIHCTQTLLEGD-GPKTYWTRELANDELILTFGADDVVCTRIYVRE
          F.EETVDGRKCRSLAT.ENENKIHCTQTL.EG..GPKTY.T.ELA.DELI..FGA.D.VCTRIYVR.
Retrocopy FDEETVDGRKCRSLAT*ENENKIHCTQTLIEGE<GPKTYCTCELASDELIMKFGAHDLVCTRIYVRK

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	8.03 RPM
SRP021940_cerebellum	0.00 RPM	4.31 RPM
SRP021940_embryo	0.08 RPM	165.10 RPM
SRP021940_placental_villous	0.19 RPM	107.91 RPM
SRP021940_synovial_membrane	0.05 RPM	47.55 RPM
SRP021940_testis	0.00 RPM	50.58 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_416 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_416 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008270	2 retrocopies	retro_ecab_894, retro_ecab_938,
Equus caballus	ENSECAG00000015978	1 retrocopy	retro_ecab_416 ,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,