RetrogeneDB ID: retro_cpor_548

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:31838185..31839527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cpor_548
GAAGGAAAGGGAATGCCTTGCCTTGCCAAGGGAGAGTCTGGAGTTTTGGGAAAAGAAGCACTTAAAGCAGGCATTGAAGC
AGGAAATATTAATATGACTTCTGAAGAAGTATTCCAAATTGAAGAACACATCAGCGAGCGCCTGGCAGAAGTGTTGGCTG
AGTTCGAAAGAAGGAAGCGAGCTCAACAAATCAATGTTTCCACAGATGACTCAGAAGTCAAGGCTTGCCTCAGAGCTGGG
GGAACCCATCATACTTTTTTGAGAGGACCCTGCTGAAAGAAGAGAAAGGTTACGAAACGTTCTCTCCGTGGGTAGTACTG
ATGCCTTAAAAAAGACAAAACAAGATGGTGAGAAATCTAAGAAATCCCAAAAAGAGTATCAGCAAACTTGGTAATGTGAA
GGACCAAACAGCCTGGAGGTGGCCAGACTGTGGATCACTAATTATTCACTACTCAGGGCAGTGAAATGCTTGGAAGAGGT
CCAGCTCCATAAAGAGATTCTTGAGACAACTAGAGCATCCCATATGCAAGAGCTGCACAGATCCCTCTGGTCTTGGAATA
ATTTCTGCCACCAGATTGGAGATGATTGACCCATCTCCTACTGCCACTGTAGTCCCAATTCTAAAATGCTAGTCATAGCT
TGTTGCAGTGGATTTTGCAATCTCTGGTCTGTTTCTGATTGTAAACTCCTTCACACTCTTTGAAGTCATCATACAAATGT
AGAAGCAATTGTATTTCATCCCAAATCCACTGTGTCATTGGACCAAAAAGATATCAACCTGGCTTTTTGTGATTCTGGGT
TTGTGAATCTTTGGAGTCTTGACAGGGCTGAACCAGCGGCAGATACTGAAGGCCATACTGTGTGTGTAGCTCAAGTAATG
TGGCATCCATCAGGACGTTTCCTGGGCACCACCTGCTCTGATCATTCAGGTGCTTAGAGGATTGGGAGGTTAAAGAGGAG
ATCCTGATTCAGGAAGGCCACAGCATGGGTGCAGATGACATTTGCCTTCCATCAAGATGGCTCTTCGGTTGGCATTGGGG
GACTGGATGCATTTGGTTGAGTTTGGGACCTGCATATGGGACGTTGCATCATGTTCCTAGAAGGCCACCTAAAGGAAATC
TCTGGGATAAGTTTCTCCCCTAATGGCTACCACATTGCAACTGGCAGTGATGAATACACCTGCAAAGTGTGGGACCTTCC
ACAGCAGTATTGTGTCTATACCATCCCTACCCATCAGAACTTGGTGACTGCGGTCCAGTTTGAGCCTGTCCATTGGAACT
TCTTGCTCATGGGCACCTACGACAGCAAAACCAAGATCTGGACCCACTCGGGGGGTCCTCCT

Alignment

ORF - retro_cpor_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 84.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEKERERLAKGESGILGKEGLKAGIEAGNINITSVGEVFEIEEHISERQAEVLAEFERRKRARQINVSTD
          E.K....LAKGESG.LGKE.LKAGIEAGNIN.TS..EVF.IEEHISER.AEVLAEFERRKRA.QINVSTD
Retrocopy EGKGMPCLAKGESGVLGKEALKAGIEAGNINMTSE-EVFQIEEHISERLAEVLAEFERRKRAQQINVSTD

Parental  DSEVKACLRALGEPITLFGEGP-AERRERLRNILSVVGTDA---DDEKSKKSK---EEYQQTWYHEGPNS
          DSEVKACLRA.G...T.F..GP.AERRERLRN.LSV..TDA.........KSK....EYQQTW..EGPNS
Retrocopy DSEVKACLRAGGTHHT-FLRGP>AERRERLRNVLSVGSTDALKKTKQDGEKSKKSQKEYQQTW*CEGPNS

Parental  LKVARLWIANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPISYCHFSPNS
          L.VARLWI.NYSL.RA.K.LEE..LHKEI.ETTR.S.MQELH.SL.S.NNFC.QIGDD.PISYCH.SPNS
Retrocopy LEVARLWITNYSLLRAVKCLEEVQLHKEILETTRASHMQELHRSLWSWNNFCHQIGDD*PISYCHCSPNS

Parental  KMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDQKDVNLASCAADGSVKLWSLDSD
          KML..AC.SG.C.LWSV.DC.LLHTL..H.TNV.AIVFHPKSTVSLDQKD.NLA.C...G.V.LWSLD..
Retrocopy KMLVIACCSGFCNLWSVSDCKLLHTL*SHHTNVEAIVFHPKSTVSLDQKDINLAFCDS-GFVNLWSLDRA

Parental  EPVADIEGHTVRVARVMWHPSGRFLGTTCYDRSWR-LWDLEAQEEILHQEGHSMGVYDI-AFHQDGSLAG
          EP.AD.EGHTV.VA.VMWHPSGRFLGTTC.D.S...L.D.E..EEIL.QEGHSMG..DI.AFHQDGS..G
Retrocopy EPAADTEGHTVCVAQVMWHPSGRFLGTTCSDHSGA<LEDWEVKEEILIQEGHSMGADDI>AFHQDGSSVG

Parental  TGGLDAFGRVWDLRTGRCIMFLEGHLKEIYGISFSPNGYHIAAGRGDNTCKVWDLRQRRCIYTIPAHQNL
          .GGLDAFG.VWDL..GRCIMFLEGHLKEI.GISFSPNGYHIA.G....TCKVWDL.Q..C.YTIP.HQNL
Retrocopy IGGLDAFG*VWDLHMGRCIMFLEGHLKEISGISFSPNGYHIATGSDEYTCKVWDLPQQYCVYTIPTHQNL

Parental  VTGVKFEPIHGNFLLTGAYDNTAKIWTHPGWSP
          VT.V.FEP.H.NFLL.G.YD...KIWTH.G..P
Retrocopy VTAVQFEPVHWNFLLMGTYDSKTKIWTHSGGPP

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	0.00 RPM	9.03 RPM
SRP017611_kidney	0.00 RPM	17.59 RPM
SRP017611_liver	0.04 RPM	7.14 RPM
SRP040447_lung	0.00 RPM	10.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_548 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_548 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,