RetrogeneDB ID: retro_cpor_1531

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_94:448832..450311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000014729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRPF4
• Ensembl ID: ENSCPOG00000010747
• Aliases: None
• Description: None

Sequence

>retro_cpor_1531
GGCTTTCTCAGAGGTTTCCCGGCTCCAGAGCCCGGCATGGCTTCTTTGCGAGCCTCTTCCACAGCAACCAAAACCAGAGC
ACCTGATGACTTCGTTGCTCCTGTTGTGAAGAAACCACACATCTATTATGGAAGTTTGGAAGACAAGGAAAGGGAACGCC
TTGCCAAGGGAGAGTCTGGAATTTTGGGAAAAGGAGGACTTAAAGCAGGCATTGAAGCAGGAAATATTAATATAACTTCT
GGAGAGGTATTTGAAATTGAAGAATCCATCAGTGAGTGGCAGGCAGAAGTATTGGCTGAGTTTGAAAGAAGGAAGCGAGC
TCGACAAATCAACGTTTCCACAGATGACTCAGAAGTCAAGGCTTGCCTCAGACCCTTGGAGGAACCCATCACACTTTTTG
GAGAGGGCCCTGCTGAAAGAAGAGAAAGGTTAAGAAATATTCTCTCAGTGGTTGGTACTGATGCCTTAAAAAAGACAGAA
AAAGATGATGAGAAATCTAAGAAGTCCAAAGAAGAGTATCAGCAAACCTGGTACCATCAAGGACCAAACATCCTGAAGGT
GGCTAGACTGTGGATTGCTAATTATTCACTGCCCAGGGCAATGAAACGCTTGGAAGAGGCCCGTCTCCATAAAGAGATTC
CTGAGACAGCTAGAACATCCCAGACGCAAGAGCTGCACAAATCCCACAGGTCTTTGAATAATTTCTGCAGCCAAATTGGG
GATGATCTGCCTATCTCCTACTGTCACTTTAGTCCCAATTCCAAAATGCTGGCCACAGCTTGTTGGAGTGGGCTTTGCAA
GCTCTGGTCTGTTCCAGATTGTAACCTCCTTCACACTCTTCGAGGTCATAATACAAATGTAGGAGCAATTGTATTTCATC
CCAAGTCCACTGTGTCATTGGATCAGAAAGATGTCAACCTGGCCTCTTGTGCTGCTGATGGGTCTATGAAGCTCTGGAGT
CTTGACAGTGATGAACCAGTGGCAGATATTGAAGGCCATACCATGCATGTAGCCCGAATAATGTGGCACCCATCAGGACG
TTTCCTGGGCACCACCTGCTATGATCGTTCATGGCGCTTATGGGATTTGGAGGCTCAAGAGGAAATCCTGCATCAGGAGG
GTCATAACATGGGTGTATATGACATTGCCTTCCATCAAGATGGTTCTTTGGCTGGCACTGGGGGCCTGGATGCATTTGGT
CGAATTTGGGACCTGCGCACAGGATGTTGCATCATGTTCCTAGAAGGCCACCTAAAGGATATCTACGGAATAAGTTTCTC
CCCCAATGGCTACCACATTGCAACTGGCAGTGGTGACAATACTTGCAAAGTGTGGGACCTTCGACAGCGGCGTTGCATCT
CTACCATCCCTGCCCATCAGAACTTAGTGACTGGGGTCAAGTTTGAGCCTATCCATGGGAACTTCTTGCTCACTGGTGCC
TATGACAACACAGCCAAGATCTGGACCCACTCAGGCTGG

Alignment

ORF - retro_cpor_1531 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.9 %
• Parental protein coverage: 92.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GFLRGFPAPEPGMASSRASSTATKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKEGLKAG
          GFLRGFPAPEPGMAS.RASSTATKT.APDD.VAPVVKKPHIYYGSLE.KERERLAKGESGILGK.GLKAG
Retrocopy GFLRGFPAPEPGMASLRASSTATKTRAPDDFVAPVVKKPHIYYGSLEDKERERLAKGESGILGKGGLKAG

Parental  IEAGNINITSVGEVFEIEEHISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPITLFGEGPAE
          IEAGNINITS.GEVFEIEE.ISE.QAEVLAEFERRKRARQINVSTDDSEVKACLR.L.EPITLFGEGPAE
Retrocopy IEAGNINITS-GEVFEIEESISEWQAEVLAEFERRKRARQINVSTDDSEVKACLRPLEEPITLFGEGPAE

Parental  RRERLRNILSVVGTDA---DDEKSKKSK---EEYQQTWYHEGPNSLKVARLWIANYSLPRAMKRLEEARL
          RRERLRNILSVVGTDA.........KSK...EEYQQTWYH.GPN.LKVARLWIANYSLPRAMKRLEEARL
Retrocopy RRERLRNILSVVGTDALKKTEKDDEKSKKSKEEYQQTWYHQGPNILKVARLWIANYSLPRAMKRLEEARL

Parental  HKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFSPNSKMLATACWSGLCKLWSVPDCNLLHT
          HKEIPET.RTSQ.QELHKS.RSLNNFCSQIGDD.PISYCHFSPNSKMLATACWSGLCKLWSVPDCNLLHT
Retrocopy HKEIPETARTSQTQELHKSHRSLNNFCSQIGDDLPISYCHFSPNSKMLATACWSGLCKLWSVPDCNLLHT

Parental  LRGHNTNVGAIVFHPKSTVSLDQKDVNLASCAADGSVKLWSLDSDEPVADIEGHTVRVARVMWHPSGRFL
          LRGHNTNVGAIVFHPKSTVSLDQKDVNLASCAADGS.KLWSLDSDEPVADIEGHT..VAR.MWHPSGRFL
Retrocopy LRGHNTNVGAIVFHPKSTVSLDQKDVNLASCAADGSMKLWSLDSDEPVADIEGHTMHVARIMWHPSGRFL

Parental  GTTCYDRSWRLWDLEAQEEILHQEGHSMGVYDIAFHQDGSLAGTGGLDAFGRVWDLRTGRCIMFLEGHLK
          GTTCYDRSWRLWDLEAQEEILHQEGH.MGVYDIAFHQDGSLAGTGGLDAFGR.WDLRTG.CIMFLEGHLK
Retrocopy GTTCYDRSWRLWDLEAQEEILHQEGHNMGVYDIAFHQDGSLAGTGGLDAFGRIWDLRTGCCIMFLEGHLK

Parental  EIYGISFSPNGYHIAAGRGDNTCKVWDLRQRRCIYTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWT
          .IYGISFSPNGYHIA.G.GDNTCKVWDLRQRRCI.TIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWT
Retrocopy DIYGISFSPNGYHIATGSGDNTCKVWDLRQRRCISTIPAHQNLVTGVKFEPIHGNFLLTGAYDNTAKIWT

Parental  HPGW
          H.GW
Retrocopy HSGW

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	0.12 RPM	9.03 RPM
SRP017611_kidney	0.21 RPM	17.59 RPM
SRP017611_liver	0.13 RPM	7.14 RPM
SRP040447_lung	0.03 RPM	10.47 RPM
SRP040447_skeletal_muscle	0.04 RPM	7.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1531 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1531 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004571	1 retrocopy	retro_btau_1341,
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819,
Cavia porcellus	ENSCPOG00000010747	2 retrocopies	retro_cpor_1531 , retro_cpor_548,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Myotis lucifugus	ENSMLUG00000015309	1 retrocopy	retro_mluc_77,
Otolemur garnettii	ENSOGAG00000007802	1 retrocopy	retro_ogar_2854,