RetrogeneDB ID: retro_ocun_1232

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:49618426..49619363(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSOCUG00000009275
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_ocun_1232
ATGGCGGATATAGACAAACTCAAGATCGACAGCATCATCCAATGGCTGCTGGAAGTGAGAGGGTCCAAGCCTGGTAAGAA
TGTTCAGCTACAGGAGAATGAAATCAGAGGACTGTGCTTAAAGTCTCGAGAATCTTTCTCAGTCAGCCTATCCTACTAAA
ACTTGAAGCACCACTCAAAATATGTGGTGACATCCATGGACAATACTATGATTTGCTGCGACTTTTTGAGTACGGTGGTT
TCCCGCCAGAAAGCAACTACCTGTTTCTTGGGGACTATGTGGACAGGGGGAAACAGTCGCTGGAGACGATCTGCCTCTTA
CTGGCCTACAAAATCAAATATCCCGAGAATTTTTTTCTTCTCAGAGGGAACCATGAATGTGCCAGCATCAATAGGACTTA
TGGATTTTATGATGAATGTAAAAGAAGATACAACATTAAACTATGGAAAACTTTCACAGACTGTTTTAACTGTTTACCGA
TAGCAGCCATCATGGATGAGAAAATCTTCTGCTGTCACGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATTCGG
TGAATTATGCGACCAACTGATGTGCCAGATCAAGGTCTTTGTGATCTTTAGTGGTCTGACCCCGATAAAGATGTCTTAGG
CTGGGGTGAAAATGACAGAGGCGTGTCCTTCACATTCAGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGATTTGG
ATCTTATACGTAGAGCCCACCAGGTGGTTGAAGATGGATATGAGTTTTTTGCAAAGAGACAGTTGGTCACTCTTTCTCTG
CACCCAACTATTGTGGAGAGTTTGACAATGCAGGTGCCATGATGAGTGTGGATGAAACACTAATGTGTTCCTTTCAGATT
TTAAAGCCTGCAGAGAAAAAGAAGCCGAATGCCACGAGACCTGTAACACCTCCACGG

Alignment

ORF - retro_ocun_1232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.2 %
• Parental protein coverage: 93.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSRE-IFLSQPILLELEAPLKICGDIHGQY
          MADIDKL.IDSIIQ.LLEVRGSKPGKNVQLQENEIRGLCLKSRE.IFLSQPILL.LEAPLKICGDIHGQY
Retrocopy MADIDKLKIDSIIQWLLEVRGSKPGKNVQLQENEIRGLCLKSRE<IFLSQPILLKLEAPLKICGDIHGQY

Parental  YDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDE
          YDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINR.YGFYDE
Retrocopy YDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRTYGFYDE

Parental  CKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDP
          CKRRYNIKLWKTFTDCFNCLPIAAI.DEKIFCCHGGLSPDLQSMEQIR.IMRPTDVPDQG.LCDL.WSDP
Retrocopy CKRRYNIKLWKTFTDCFNCLPIAAIMDEKIFCCHGGLSPDLQSMEQIR*IMRPTDVPDQG-LCDL*WSDP

Parental  DKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTL-FSAPNYCGEFDN
          DKDVLGWGENDRGVSFTF.AEVVAKFLHKHDLDLI.RAHQVVEDGYEFFAKRQLVTL.FSAPNYCGEFDN
Retrocopy DKDVLGWGENDRGVSFTFSAEVVAKFLHKHDLDLIRRAHQVVEDGYEFFAKRQLVTL<FSAPNYCGEFDN

Parental  AGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR
          AGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR
Retrocopy AGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPR

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	119.92 RPM
SRP017611_kidney	0.10 RPM	70.85 RPM
SRP017611_liver	0.00 RPM	48.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1232 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1232 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232 , retro_ocun_665,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,