RetrogeneDB ID: retro_cpor_137

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:70737762..70738592(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000024984
• Aliases: None
• Description: None

Sequence

>retro_cpor_137
ATGGCAAGACGGCCTCATCCCTGTGACGGTAACTTCCGTGATCTAGAAAACTGGAATCAGAAATTGCATAATAGACTTTG
TAAACTTTACAAACATTCAAGTATTCCTCACATGTTACTAAAGGAGGAGTAGACAACACCAAAATGAGACCACGTGGTGT
TAGTGGGGAACATGAGAGATGAAGAGACAAGCAAGGATCAAATGACAGATCACGAGATTCATCTCATGAAAGAACAGAAT
CTCAACTAACTCCTTGCTTTAGAAACGTTGCTTCTCCAATACAGCAGCATCATGTTGAAAGAGAAAAAAGGTCATAGTTC
CTCTCTTCCAAGCAGTCCTTCTCCTCAGAAATTATCTCCAAACGGTTCAATTAGCAGTGCTGGGAACAGCAGCAGAAACA
GTAATCAGTCAAGTTCAGATAGTAGCTGTAAGACAACCAGAAAGATAGTATTTGTACACGAAAATGCAAAAGACGGTGCT
CAGGATATACGAACTCCAGAACAAGTGGCATTAATAGTGGATAGCAGTAGACTTGTGGTCCACCCATCCATTCTTACTGC
ACAGCCAAATCCAGTGTTGGGCAGGATGCTTGGGTCTGGCCGAGAACATAACTTTACACCTCCCACAATAAAGGAGAGTA
TGAAGTGGCAGAAGGAATTGGTTCTACTGTATTTTGAGCTCTTATGGATTCCTGTAAGACAGGAATAATTCATTGTCCTG
ATGGCATATCTATTCCTGAGCTGAGAAAAGAATGTGATTATCTCTGTATCTCTTTTGACTATAGCACTATTTTAAAAATG
AATATAGCACTATTAAATGTAGAGATCTCA

Alignment

ORF - retro_cpor_137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 58.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAGRPHPYDSNSSDPENWDRKLHSRPRKLYKHSSA-SSRVAKGGVDNTKMSLHGASGGHERSRDRRRSSD
          MA.RPHP.D.N..D.ENW..KLH.R..KLYKHSS..SS.V.KGGVDNTKM...G.SG.HER.RD...S.D
Retrocopy MARRPHPCDGNFRDLENWNQKLHNRLCKLYKHSSI<SSHVTKGGVDNTKMRPRGVSGEHER*RDKQGSND

Parental  RSRDSSHERTESQLTPCIRNVTSPTRQHHVEREK-DHSSSRPSSPRPQKASPNGSFSSAGNS-RNSSQSS
          RSRDSSHERTESQLTPC.RNV.SP..QHHVEREK..HSSS.PSSP.PQK.SPNGS.SSAGNS.RNS.QSS
Retrocopy RSRDSSHERTESQLTPCFRNVASPIQQHHVEREK>GHSSSLPSSPSPQKLSPNGSISSAGNSSRNSNQSS

Parental  SDGSCKTPGEMVFVYENAKEGARNIRTSERVTLIVDNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRP
          SD.SCKT....VFV.ENAK.GA..IRT.E.V.LIVD..R.VV.PSI.TAQPN..LGRM.GSGREHNFT.P
Retrocopy SDSSCKTTRKIVFVHENAKDGAQDIRTPEQVALIVDSSRLVVHPSILTAQPNPVLGRMLGSGREHNFTPP

Parental  -NEKGEYEVAEGIGSTVFRAILDYYKTGIIRCPDGISIPELREACDYLCISFEYSTIKCRDLSALMHELS
          ...KGEYEVAEGIGSTVF.A..D..KTGII.CPDGISIPELR..CDYLCISF.YSTI.......L..E.S
Retrocopy <HNKGEYEVAEGIGSTVF*ALMDSCKTGIIHCPDGISIPELRKECDYLCISFDYSTILKMNIALLNVEIS

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	23.29 RPM
SRP017611_kidney	0.00 RPM	3.45 RPM
SRP017611_liver	0.00 RPM	2.79 RPM
SRP040447_lung	0.00 RPM	9.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.41 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_137 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_137 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137 ,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,