RetrogeneDB ID: retro_ecab_732

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:95908992..95909434(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIF
• Ensembl ID: ENSECAG00000008796
• Aliases: None
• Description: peptidylprolyl isomerase F [Source:HGNC Symbol;Acc:9259]

Sequence

>retro_ecab_732
CTTGGGCTGCATCTTCTTCAAGCTGTTTGCAGAAAAGTTCCAAAGACAGCAGAAAACTTTCGTACTCTGAGCAGTGAGGA
GAAAGGATTTGGTTATAAAGTTTCCTGCCTTAACAGAATTATTCCAGGATTTATATGCCAGAGTGGTGACTTCACACGCC
ATAATGGCACTGGCGACAAGTCCATCTGTGGGGAGAAATTTGATGATGAGAATTTCATCCTGAAGCATACGTGTCCTGGC
ATCATGTCCATGACAAATATTGGACCCAACACAAATGGTTCCCAGTTTTTCACCTGCACTGCCAACACTGAGTGGTTGGA
TGGCAAGCCTGTGGTCTTTGGCAAAGTGAAAGAGGGCATGAATATCGTGGAAACATGGAGCCTTTGGGTCCAGGATTCGC
AAGACCAGCAAAAAGATCACCACTGCTGACTGAGGACAAATC

Alignment

ORF - retro_ecab_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.0 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGRVVLELNADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPAFMCQAGDFTNHNGTGGKSIYGSRFPDE
          LG...L......VPKTAENFR.L...EKGFGYK.S...R.IP.F.CQ.GDFT.HNGTG.KSI.G..F.DE
Retrocopy LGLHLLQAVCRKVPKTAENFRTLSSEEKGFGYKVSCLNRIIPGFICQSGDFTRHNGTGDKSICGEKFDDE

Parental  NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVKEGMDVVK-KIESFG-SKSGKTSK
          NF.LKH..PG..SM.N.GPNTNGSQFF.CT..T.WLDGK.VVFG.VKEGM..V....E..G.S...KTSK
Retrocopy NFILKHTCPGIMSMTNIGPNTNGSQFFTCTANTEWLDGKPVVFGKVKEGMNIVE<NMEPLG<SRIRKTSK

Parental  KIVITDCGQL
          KI...D.GQ.
Retrocopy KITTAD*GQI

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	0.06 RPM	0.83 RPM
SRP021940_cerebellum	0.16 RPM	9.56 RPM
SRP021940_embryo	0.10 RPM	8.75 RPM
SRP021940_placental_villous	0.10 RPM	1.78 RPM
SRP021940_synovial_membrane	0.14 RPM	4.12 RPM
SRP021940_testis	0.26 RPM	2.62 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_732 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_732 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732 ,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,