RetrogeneDB ID: retro_ecab_617

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:28670032..28670673(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004955
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIB
• Ensembl ID: ENSECAG00000017164
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase B [Source:RefSeq peptide;Acc:NP_001093231]

Sequence

>retro_ecab_617
ATGCCGCATTTCTCAGAGCCGAATATGAAGGTGTTCTTTGCTGCCGCCCTTATCAAGGGCTCAGTCTTTTTCCTGCTGTT
GTCAGGACCCTCCACGGCTGATGAGAAGGGACCCAAAGTCACTGTCAAGGTGTGCATTGATCTGAGAATTGGAGGTAAAG
ATCAGGCTGGATGGTCATTGGTCTCTTTGGAAAGACTCTTCCAAAAACCCTGGATAATTTTGTGGCCTTAGCCACAAGAT
AGAAAGGATTTGGGTACAAAGACAGCAAATTCCATCATGTGAGCAAGGACGTCACGATCCAGGGTGGAGACTTCACCCGG
GGAGATGGCACTGGAGGTAAGAGCATCTAAGGTGAAGGCTTCTTGGATGAGAACTTCAAGCTGAAACACTATGGGCCCGG
CTGGGTAAGCATGGCCAACACAGGCAAAGACTCCAACGGCTCCCAAGTCTTTATCACGACAGTCAAGACAGCCTGGCTAG
ATGGCAAGCACATCGTGTTCGGCAAAGTTCTTCAGGGCATGGAGGTAGTGCGGAAGGTGGCGAGAGCCAAGACAGATGGT
CAGGACAAGCCCCTGAAGGATGTGACAATCGCAGACTGCGGCAAGATCCAGGTGGAGAAGCCCTTTGCCATCGCCAAGGA
G

Alignment

ORF - retro_ecab_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRFSERNMKVLFAAALIVGSVFFLLLPGPSTADEKKKGPKVTVKVYFDLRIGDED-IGRVVIGLFGKTV
          M..FSE.NMKV.FAAALI.GSVFFLLL.GPSTADEK..GPKVTVKV..DLRIG..D..G..VIGLFGKT.
Retrocopy MPHFSEPNMKVFFAAALIKGSVFFLLLSGPSTADEK--GPKVTVKVCIDLRIGGKD<SGWMVIGLFGKTL

Parental  PKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVS
          PKT.DNFVALAT..KGFGYKDSKFH.V.KD..IQGGDFTRGDGTGGKSI.GE.F.DENFKLKHYGPGWVS
Retrocopy PKTLDNFVALATR*KGFGYKDSKFHHVSKDVTIQGGDFTRGDGTGGKSI*GEGFLDENFKLKHYGPGWVS

Parental  MANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVRKVETTKTDGRDKPLKDVTIADCGKIEVEK
          MAN.GKD.NGSQ.FITTVKTAWLDGKH.VFGKVL.GMEVVRKV...KTDG.DKPLKDVTIADCGKI.VEK
Retrocopy MANTGKDSNGSQVFITTVKTAWLDGKHIVFGKVLQGMEVVRKVARAKTDGQDKPLKDVTIADCGKIQVEK

Parental  PFAIAKE
          PFAIAKE
Retrocopy PFAIAKE

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	0.30 RPM	516.45 RPM
SRP021940_cerebellum	0.00 RPM	134.14 RPM
SRP021940_embryo	0.05 RPM	338.71 RPM
SRP021940_placental_villous	0.29 RPM	336.54 RPM
SRP021940_synovial_membrane	0.22 RPM	442.64 RPM
SRP021940_testis	0.00 RPM	184.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_617 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999,
Equus caballus	ENSECAG00000017164	1 retrocopy	retro_ecab_617 ,
Echinops telfairi	ENSETEG00000012671	1 retrocopy	retro_etel_1493,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413,