RetrogeneDB ID: retro_cpor_370

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_134:2931436..2932360(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL4
• Ensembl ID: ENSCPOG00000003055
• Aliases: None
• Description: None

Sequence

>retro_cpor_370
GAGCTGTCCAGCTAAAATGTCACTTTGTCTGTTACCTTCAAGGCTCCCATTTGACCAGATGTTGTGAACTTTGTTCACAT
CACCTTGCCTACAAACAAAAAGCAGTCTATGCTGTCAGCAAATTAGAAAATCAACAGACCAGTGCCCAGTCTTGGATGAC
TGCCAGAACTGTGACTCGAGTTCCCAGAGTTCATGGTGGTGGACACACCTTTCCAGCCAGAGTGCTTTGGAAACAAGTAT
TGAGAAGGTTGCATATTTGCACCAACCCAAATCTGGTGCTGTTGGCAACGCAAAGTGTACACAACTCAGAAGCAATATGC
CATCTTCTCTGCCTTGGCTGCCTCAGCCCTGCCAGTGCTGCTCCTGTGGAAAGGTCATCGAATGGAGGAAGTTCCTGAAC
TGCCTTTGATGGTGGAAGATAAAGTTGAAGGTTATAAGAAAACTAAGGAGGCAGTTGTGCTTCTGAAGAAACGTAAGGCC
CAGAATGATTACAAAAAGTTCTATGTCTCTCAGCCAATGAGGGCTGGCAAGAGCAAGGAGGGAACCCACTGTAGGATCCA
AAGCAAGGATTTTGCATCATCTATAATGAAGACAATGGCATCATCAAGGTCTTCAGAAATATCCCGGGCACTACTCTGCT
TAAAGTAAGCAACTGAATATTGTGAAATTTGCCCCTTGTGGGCATGTGAGGTGCTTCTGCATTTGGACTGAGAGTGCTTT
CTGGAAGTTAGATGTGTTGTAGGGTACTTGGCGTAAAGCTGCTACCCTCAAGAGTCACTATAACCTTCCTATGCACAAGA
TAAGCAATGCAGACCTGAGAAAATCATGAGGAGCCTAGACAAATAAAGAACCCTGCAAGCACCTTGCATGAAAATTCACC
ATAGGGTCCTGAAAAAGAATCCTCTGAAGAATTTGAGGATCTTG

Alignment

ORF - retro_cpor_370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.35 %
• Parental protein coverage: 86.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQP-YAVSELAGHQTSAESWGTGRAVARIPRVRGGG-
          E.S..NVTL...FKAPI.PD.VNFVH..L..N..Q..YAVS.L...QTSA.SW.T.R.V.R.PRV.GGG.
Retrocopy ELSS*NVTLSVTFKAPI*PDVVNFVHITLPTNKKQS<YAVSKLENQQTSAQSWMTARTVTRVPRVHGGG<

Parental  THRSGQGA-FGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPL
          TH.S.Q.A.FGN....G..FAPT..W..W.R.V.TTQK.YAI.SALAASALP.L...KGHR.EEVPELPL
Retrocopy THLSSQSA<FGNKY*EGCIFAPTQIWCCWQRKVYTTQKQYAIFSALAASALPVLLLWKGHRMEEVPELPL

Parental  VVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRK-GPCIIYNEDNGIIKAF
          .VEDKVEGYKKTKEAV.LLKK.KA.ND.KK.Y.SQ.MRAGK.K.....RIQ.K.G.CIIYNEDNGIIK.F
Retrocopy MVEDKVEGYKKTKEAVVLLKKRKAQNDYKKFYVSQPMRAGKSKEGTHCRIQSK<GFCIIYNEDNGIIKVF

Parental  RNIPGITLLNVS-KLNILKLAPGGHVGRFCIWTESAFRKLDELYGTWRKAATLKSHYNLPMHKMINTDL-
          RNIPG.TLL.VS..LNI.K.AP.GHV..FCIWTESAF.KLD.L.GTWRKAATLKSHYNLPMHK..N.DL.
Retrocopy RNIPGTTLLKVS<QLNIVKFAPCGHVRCFCIWTESAFWKLDVL*GTWRKAATLKSHYNLPMHKISNADL<

Parental  SRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIM
          ..I..S....R.L.AP..KIH.RVLKKNPLKNLRI.
Retrocopy EKIMRSLDK*RTLQAPCMKIHHRVLKKNPLKNLRIL

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	238.64 RPM
SRP017611_kidney	0.00 RPM	386.82 RPM
SRP017611_liver	0.00 RPM	210.58 RPM
SRP040447_lung	0.00 RPM	367.49 RPM
SRP040447_skeletal_muscle	0.01 RPM	631.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_370 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_370 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 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Cavia porcellus	ENSCPOG00000003055	1 retrocopy	retro_cpor_370 ,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Mus musculus	ENSMUSG00000032399	2 retrocopies	retro_mmus_2863, retro_mmus_495,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Oryctolagus cuniculus	ENSOCUG00000008794	3 retrocopies	retro_ocun_1134, retro_ocun_630, retro_ocun_631,
Ochotona princeps	ENSOPRG00000007792	1 retrocopy	retro_opri_735,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,