RetrogeneDB ID: retro_cpor_242

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_108:3316135..3317701(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000014231
• Aliases: None
• Description: None

Sequence

>retro_cpor_242
AGATGGAACCTGGCTGAGAGATCTGAGGCTAGTTTGAAGGTATAGGCATCAGGTGTGAGTTCTGAAGGAGCAGGAGAAAA
ACTGGGCTTTTCAGATTTTCTTGAGCCTGTTGGAACTTCATCGGCTGCTGTGAAAAAGCAGCTGATAGAGTTAAATCCAA
GGAGCTATGGATTCACCCCTTAACAAAGAGGTTAAACAGATCCACAGAGAAGTAACATTCAATCAAACATCACCAGTCCT
CTCCAAATGTGATCCAGTTATTCTCAAGAACCAGCCAGCAGAGCAGCTGGGGTTTCCCTGGAGAAGCAGCAGTCAGCCTT
TGCTCCCACAGAACTCGTCTTCAGTGAGTAGAAGGCAAGAATCCTTCTGGAACAGGAAGCGATTAGTCTCCATTCAAACA
AGCAGCCCTGGTGACAGACCCTTTATTGGCTCCCATTAAAAAGGCCTCGTTCCGGCTACAAGCCTGGAAGAGGCTAAGGA
GCCCCAAGCAGAGAGCTCCAGAAGGCCTGGACTTTGCAGCCCTACTGTGAAACCAGGGCACAAAGGGAGAAGAAAATCAA
AGGTAAAAATTTCACAGAATTGTAAAGAAAGAAGAAGCCAAGAAAGCCCTAAAGGACTTTGATTGGCTGTGGAAGGTGAA
TGCTACTGCTGCATTGGAGCTACTGGACGGAATTGGAAAGGCCAGAACGCTGGAAGGTGTGAGCCTGCAGCACCAGGACG
TGGGAAACAGGATGACTCAAAGACAATTATGGCCAACTATGACTTGGAGGCTCCCTAAGGTTGGCAGGAACATTGGCTAA
GAACAGAGAAGTGACACAGCCACTCCAGATAATCTCAGAAAGTGAAGAAGAGGAGAGGGGTGCCAAAGAGGAAGAACCTC
TTGTCCCTGATGGAGTGGATGCAGTGCAGATGTGTTCAGATGGACCAAATCCGCGGAGGCTCAAGAATTCTAATAGTGAC
GCAAAAGCAGGTGAAATCCAGACAGACCCAGGACAACAACCTGAGCCTGTCGTCCAGACATTTTCTAAAAGTGAGCAAGA
TGAAAGACCAGCAGCAGAGGGAGAAATTCTGTTGAAGAATTTGAAGAAATCTGCTCCCTTAGAAAAAGATCTGAGCTCAA
CCAGGATAGTGAGCCAGTGGGCAGCCAGGAAACAGAAGACTGTAGCAGCCAGGACATATTACTGAATGGAACTGAGTCAG
AAATTCAGCAAGGAAACCATCAGTCCTGGAAGCCAACAGTCCAGCAAGGACTGTTCTTCAGGTTGGGAGAGAGGGATGTG
CCCCAGAAGAGGAATCTCTGTTGCTTCAGAGGCCAGAGAGAGTAAAGCTTCTGGGAGAACCAGAAGACCTGGGTAAAGAA
GGATATTTCCAAAATCAGGAGCTTCCCACACCTTTGTTAAAATGGGAACAAATGAAGAGAAACCCAAATAACCAGACTGA
TGCCCCAAAGAGGGTGAAAAAGAAGGAGCAAATGATTGATTTCCAGAATCTCCTAAGTGCAGAATCTCCTTTCAAAAGTT
CTTGGCCATTCCCACAATAGAGGACTTTGAAGAGAAGGAGGAGAGA

Alignment

ORF - retro_cpor_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.15 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  RWKLAERSEASLKVSEFNVSSEGSGEKLLLSDLLEPAKTSSSLAAVKKQL-SRVKSKK-AVELPLNKQEV
          RW.LAERSEASLKV....VSSEG.GEKL..SD.LEP..TSS..AAVKKQL..RVKSK..A...PLNK.EV
Retrocopy RWNLAERSEASLKV*ASGVSSEGAGEKLGFSDFLEPVGTSS--AAVKKQL<DRVKSKE<AMDSPLNK-EV

Parental  ERINREVAFNKTSQTLSKWDPIVLKNRQAEQLVFP-LEKEPASFVPIEHVFGSWKARTPLEQEIFNIL-Y
          ..I.REV.FN.TS..LSK.DP..LKN..AEQL.FP.LEK....F.P.E.VF...KAR..LEQE.......
Retrocopy KQIHREVTFNQTSPVLSKCDPVILKNQPAEQLGFP<LEKQQSAFAPTELVFSE*KARILLEQEAISLH<F

Parental  KNKQPVTDPLLTPMEKASLKAMSLEEAKMRRA-ELQRARALQSYYEAKARRMFKKRDS-KYHKIVKKGKV
          K....VTDPLL.P..KAS...............ELQ.A..LQ.Y.E..A.R..K.....K.H.IVKK...
Retrocopy KQAALVTDPLLAPIKKASFRLQAWKRLRSPKQ>ELQKAWTLQPYCETRAQREKKIKGK<KFHRIVKKEEA

Parental  KKALKEFEQLQKVNPAAALEELEKIEKARMMERMSLKHQN-SGKWAKSKAIMAKYDLEARQAMQEQ-LAK
          KKALK.F..L.KVN..AALE.L..I.KAR..E..SL.HQ...GK...SK.IMA.YDLEA....QE..LAK
Retrocopy KKALKDFDWLWKVNATAALELLDGIGKARTLEGVSLQHQD<RGKQDDSKTIMANYDLEAP*GWQEH<LAK

Parental  NKELTQKLQVVSESEEEEKGTEEEELLVPDAVNEIQMCTDGPNPWMLRNCNSDAK-GEIQKDPEQPPEPM
          N.E.TQ.LQ..SESEEEE.G..EEE.LVPD.V...QMC.DGPNP..L.N.NSDAK.GEIQ.DP.Q.PEP.
Retrocopy NREVTQPLQIISESEEEERGAKEEEPLVPDGVDAVQMCSDGPNPRRLKNSNSDAKAGEIQTDPGQQPEPV

Parental  VQEVSESEEEEKPGGEEEVLL-QEFEERRSLRKSSELSKNAEPVGSQKTKDSSSQEVLSELKALTQKLNQ
          VQ..S.SE..E.P..E.E.LL..EFEE..SLRK.SEL....EPVGSQ.T.D.SSQ..L..L........Q
Retrocopy VQTFSKSEQDERPAAEGEILL<EEFEEICSLRKRSELNQDSEPVGSQETEDCSSQDIL--LNGTESEIQQ

Parental  KNCQSKKQNVNLVKTVLQGQREECAPEE-EEPLLLQRPERVQTLEDLEDLDHEEYSQIRELSRPVLEGER
          .N.QS.K..V........G.R....P...EE.LLLQRPERV..L...EDL..E.Y.Q..EL..P.L..E.
Retrocopy GNHQSWKPTVQQGLFFRLGERD--VPQK<EESLLLQRPERVKLLGEPEDLGKEGYFQNQELPTPLLKWEQ

Parental  TERTTDNQTDASKG-KKKEQMIDLQNLLTTKSPSVKS-LAVPTAIEELEDEEEK
          ..R...NQTDA.K..KKKEQMID.QNLL...SP...S.LA.PT.IE..E..EE.
Retrocopy MKRNPNNQTDAPKRVKKKEQMIDFQNLLSAESPFKSS<LAIPT-IEDFEEKEER

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	14.32 RPM
SRP017611_kidney	0.00 RPM	15.91 RPM
SRP017611_liver	0.00 RPM	8.66 RPM
SRP040447_lung	0.00 RPM	15.84 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_242 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_242 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242 ,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,