RetrogeneDB ID: retro_cpor_179

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:50769461..50771035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSCPOG00000021670
• Aliases: None
• Description: None

Sequence

>retro_cpor_179
CAAGAAGTTTCTGTGGCACTGAAACAAGGCCAAATTTCGCCAATAGAACTCTGTTGCAAATGTCTGTCCCTTAGCCAGAA
AGCCGAGTTTCTGAATGCTTACATTATTGTGTCAGAAGAGGTGGCCTTAAAGCAAGCTGAAGAATCAGAAAAAAAGGTAT
AAGAAAGGTCAATCACTTGGGGATTTAGATGGAATTCCTATTGCAGTAAAAGACAATTTTAGCACAGCTAGTATGGAGAC
AACACGTGCATCGAATATGCTAAAAGGTTATAGATCACCTTTGAATGCTACAGTGCTTAGAAATTGTCGGATCAGGGAGC
TGTACTAGTGGGAAAAACAAATTTAGATGAGTTTGCTATGGGCTTTGCAAGCACAAATGGTGTATCCGGGCCAGTGAAGA
ACCGCTGGAGTTACTGGAAACAACACAGAGAACAGAGGTGGCAGAATTCCCATGGTGAATGTCAGGGTGCCGACTGGCTG
ACCTTTGGAGGAAGCTCTGGCCAAAGCTGGGGCAGGAGCTCGACTGCTGTCTCAGCATTCACACGCTTTATGGCTTTAGC
ATAAGACACTGGAGGATCAAGGTGAAATCCTGCTGCCCACTGTAGGCTTGTAGGTTTTAAATCCAGCGGTGGCTTAGTTT
CTCATCATGATCTCATTCCCTGGTGAATTCGATGGATGTACCAAGAATCGTAACCAGATGTGTGGAGGATACAGTGATTG
TATTGGGTGTACTGGCTGGACATGACCCCAAAGATTCTACCACGGGGCAAGATCCAGGTAAACCATTTATGTTTCCTAGT
TTGACAGATATGCACAAACTATGTGTAGGAACTCCAAAGGAGAATCTCGTACCTGAATTATCCAGGGAAGTATGACCTCT
CTGGGGCAAAGCTGCTGGCCACTTTAAGTCTGCAGGAACCAAAGTGATTAAAGTATCCCTGCCTTACAACTCTTATTCAA
TTGTCTGCTACTGTGTTTTGTGCACATCAGAAGTGATATCAAATATAGCAAGACTTGATGGCCTAGAATATAGTCATAGA
TGTGCCATTAAAGGGTCTACTGAAGCCATGTAAGCTGCCACCAGGCGGTCAGGGTTCAGTGACGTCGTCAGAGGAAAAAT
TCTTTCAGGAAACTTTTTCTTACTAGAAGCAAACTATGAAAAGCATTTCATCAAAGTCCAGAAAGTGAGGCTCCTCATTG
CAAATGATTTGGAGAACATTTTTAACTCTGGAGTGGATGTCTTCCTGATCCCACCATCTTGAGTGAGGCAGTACCGCTCT
TGGAGTTTATCAAAGAAGACAACTGAACAGAGAGTTTCCAAGATGGTATTTTTACACAGGCAGTCAGTATGGTGGTGTTG
CCTGCTGTGAGCGGCCAACAGCCCTCTCACCCAGGGGCTGCCAATAGGCAGCCTGCTGTTCACCCAAGGTGCATTTTGTG
ACCAAAAGCTTCTCACAGTTGCCGAATGGTTTGAAAAATAAGTACAGTTTCCTATTATACAACTTCAAGAACTCATAGAG
GATTGTTTGTTAGTCTTTGAAAATAAAAGGTTAACTTCTGTTTCTCTAAAACAG

Alignment

ORF - retro_cpor_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.1 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KKVSVALKQGQITPTELCRKCLSVIQKTKFLNAYITVSYEVALKQAEESEK-RYKKGQSLGELDGIPVAV
          ..VSVALKQGQI.P.ELC.KCLS..QK..FLNAYI.VS.EVALKQAEESEK.RYKKGQSLG.LDGIP.AV
Retrocopy QEVSVALKQGQISPIELCCKCLSLSQKAEFLNAYIIVSEEVALKQAEESEK>RYKKGQSLGDLDGIPIAV

Parental  KDNFSTAGIETTCASNMLKGYIPPFNATVVQ-KLLDQGAVLMGKTNLDEFAMGSGSTDGAFGPVKNPWSY
          KDNFSTA..ETT.ASNMLKGY..P.NATV...KL.DQGAVL.GKTNLDEFAMG..ST.G..GPVKN.WSY
Retrocopy KDNFSTASMETTRASNMLKGYRSPLNATVLR<KLSDQGAVLVGKTNLDEFAMGFASTNGVSGPVKNRWSY

Parental  SKQYREQRRLRSPGERRGADEDWLIAGGSS----GGSAAAVAAATCFAALGSDTGGSTRNPAAHCGLVGF
          .KQ.REQR...S.GE..GAD..WL..GGSS....G.S..AV.A.T.F.AL..DTGGS..NPAAHC.LVGF
Retrocopy WKQHREQRWQNSHGECQGAD--WLTFGGSSGQSWGRSSTAVSAFTRFMALA*DTGGSR*NPAAHCRLVGF

Parental  KPSYGLVSRYGLIP-LVNSMDVPGILTRCVDDAAAVLGVLAGHDPKDSTTVQDPVKPFVLPSLTDVSKLC
          K.S.GLVS...LIP.LVNSMDVP.I.TRCV.D...VLGVLAGHDPKDSTT.QDP.KPF..PSLTD..KLC
Retrocopy KSSGGLVSHHDLIP<LVNSMDVPRIVTRCVEDTVIVLGVLAGHDPKDSTTGQDPGKPFMFPSLTDMHKLC

Parental  VGIPKEYLVPELSSEVRSLWSKAAGLFESAGAKVIDVSLPHTSYSIVCYHVLCTSEVASNMARFDGLEYG
          VG.PKE.LVPELS.EV..LW.KAAG.F.SAG.KVI.VSLP..SYSIVCY.VLCTSEV.SN.AR.DGLEY.
Retrocopy VGTPKENLVPELSREV*PLWGKAAGHFKSAGTKVIKVSLPYNSYSIVCYCVLCTSEVISNIARLDGLEYS

Parental  HRCDINESTEAMYAATRREGFNDVVRGRILSGNFFLLKENYENYFIKAQKVRRLIANDFVNVFNSGVDVV
          HRC.I..STEAM.AATRR.GF.DVVRG.ILSGNFFLL..NYE..FIK.QKVR.LIAND..N.FNSGVDV.
Retrocopy HRCAIKGSTEAM*AATRRSGFSDVVRGKILSGNFFLLEANYEKHFIKVQKVRLLIANDLENIFNSGVDVF

Parental  L-TPTTLSEAVPFLEFIKEDNRTRSAQDDIFTQAANMAGVPAVS-VPAGLSP-QGLPIG-LQFIAPAFGD
          L..PT.LSEAVP.LEFIKEDN.T.S.QD.IFTQA..M...PAVS..P..LSP.QGLPIG.L.F...AF.D
Retrocopy L<DPTILSEAVPLLEFIKEDN*TESFQDGIFTQAVSMVVLPAVS<RPTALSP<QGLPIGSLLFTQGAFCD

Parental  QKLLTVAKWFEKQIQFPVTQLQELTEDCPSGFENDNSASVFLKQ
          QKLLTVA.WFEK..QFP..QLQEL.EDC...FEN....SV.LKQ
Retrocopy QKLLTVAEWFEK*VQFPIIQLQELIEDCLLVFENKRLTSVSLKQ

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	12.77 RPM
SRP017611_kidney	0.00 RPM	23.66 RPM
SRP017611_liver	0.00 RPM	8.36 RPM
SRP040447_lung	0.00 RPM	11.83 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.19 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_179 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_179 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 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179 ,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031, retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100, retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,