RetrogeneDB ID: retro_ocun_892

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:26686032..26687095(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025788
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIL4
• Ensembl ID: ENSOCUG00000007696
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 4 [Source:HGNC Symbol;Acc:15702]

Sequence

>retro_ocun_892
GTTAAGAAAATTAATGAGACCTTTGTTGACAAGGACTTTGTACCATATCAAGATATAAGGATAAATCATACAGTGATTTT
AGATGATCCATTTGATGACCCTCCTGATTTATTAATTCCTGATCAATCACCGGAACCCACAAGGGAACAATTAGATAGTG
GCCAAATAGGAGCAGATGAAGAAATTGATGATTCTAAAGGAAGATCAGCTGAAGAAGTAGAAGAAATAAAGGCAGAAAAA
GAAGCCAAAACTCAAACTATTCTTCTAGAGATGGTGGGAGACCTACCTGATGCAGCTATTAAACCTCCAGAAAATATGCT
GTTTGTTTGTAAATTGAATCCAGTGACCACAGACGAGGATCTGGAAATAATATTCTCAAGATTTGGGCCAATAAGAAGTT
GTGAGGTTATCCGGGATTGGAAGACAGGAGAGTCCCTCTGTTATGCTTTTATTGAATTTGAAAAGAAAAAAGATTGTGAG
AAAGCGTTCTTTAAAATGGACAATGTACTTATAGATGACAGAAGAATACACGTGGATTTTAGCCAGTCTATTGCAAAGGT
TAAGTGGAAAGGAAAGGGTGGGAAATACACTAAGAGTGATTTCAAGGAGTATGAAAAGGAACAGGATAAACGCTCTAATT
TGGTCCTGAAAGATAAAGTAAAACCCAAACAGGATGCAAAATACGATCTAATCCTAGATGAGGAGGCAGAAGACAAAGTC
CAGTCACTCACACACCAGTAAAAAACACAAGAAGAAAAGCCGGCACTGCTCTGAAGAGAAGGAAGATGAGGACTACATGC
CGGTCAAAAATACTAACCAGGATATCTACAGGGAGATGGGGTTTGGTCACTATGAAGAAGAAGAAAGCTGTTGGGAGAAA
CAAAAGAATGAAAAGAGAGACCGACCTCAGAACCAAAGTCGCAGCCGATCTCGAGAAAGGGATGGCGACTGTAGCAATAG
TCACAGGTCCAAGTACCACACTGACTCTTACGTAAGAGAGAGGGGTAAGAGGAGAGGCCGGAGCAGAAGTCCAAAGAAAT
CTAAAGAAAAATCCAAGTACAGA

Alignment

ORF - retro_ocun_892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSA
          VKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPD.SPEPTREQLDSG.IGADEEIDD.KGRSA
Retrocopy VKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPDQSPEPTREQLDSGQIGADEEIDDSKGRSA

Parental  EEVEEIKAEKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDW
          EEVEEIKAEKEAKTQ.ILLEMVGDLPDA.IKPPEN.LFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDW
Retrocopy EEVEEIKAEKEAKTQTILLEMVGDLPDAAIKPPENMLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDW

Parental  KTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWKGKGGKYTKSDFKEYEKEQDK
          KTGESLCYAFIEFEK..DCEKAFFKMDNVLIDDRRIHVDFSQS.AKVKWKGKGGKYTKSDFKEYEKEQDK
Retrocopy KTGESLCYAFIEFEKKKDCEKAFFKMDNVLIDDRRIHVDFSQSIAKVKWKGKGGKYTKSDFKEYEKEQDK

Parental  RSNLVLKDKVKPKQDAKYDLILDEEAEDSKSSHSH-TSKKHKKKTRHCSEEKEDEDYMPVKNTNQDIYRE
          RSNLVLKDKVKPKQDAKYDLILDEEAED...S..H...K..K.K.RHCSEEKEDEDYMPVKNTNQDIYRE
Retrocopy RSNLVLKDKVKPKQDAKYDLILDEEAEDKVQSLTH>SKKHKK-KSRHCSEEKEDEDYMPVKNTNQDIYRE

Parental  MGFGHYEEEESCWEKQKNEKRDRTQNRSRSRSRERDGDYSNSHKSKYHTDSYERERGKRRGRSRSPKKSK
          MGFGHYEEEESCWEKQKNEKRDR.QN.SRSRSRERDGD.SNSH.SKYHTDSY.RERGKRRGRSRSPKKSK
Retrocopy MGFGHYEEEESCWEKQKNEKRDRPQNQSRSRSRERDGDCSNSHRSKYHTDSYVRERGKRRGRSRSPKKSK

Parental  EKSKYR
          EKSKYR
Retrocopy EKSKYR

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
SRP017611_brain	0.17 RPM	14.68 RPM
SRP017611_kidney	0.00 RPM	12.06 RPM
SRP017611_liver	0.00 RPM	6.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_892 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_892 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019613	1 retrocopy	retro_cjac_2963,
Macaca mulatta	ENSMMUG00000023067	1 retrocopy	retro_mmul_1715,
Nomascus leucogenys	ENSNLEG00000015316	1 retrocopy	retro_nleu_173,
Oryctolagus cuniculus	ENSOCUG00000007046	2 retrocopies	retro_ocun_1493, retro_ocun_1759,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892 ,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413,
Taeniopygia guttata	ENSTGUG00000010655	1 retrocopy	retro_tgut_16,