RetrogeneDB ID: retro_cpor_671

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:21194840..21195368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC1
• Ensembl ID: ENSCPOG00000000876
• Aliases: None
• Description: None

Sequence

>retro_cpor_671
TCAGACACTAAAGAAGAAAGCTGAAAAAAGAGCAAAAAGAGACATCACAGTCATCTTCTAACAGTTATTCAGATAGTAAA
ATATACAGCTGATAGAAAGGTGGAAGGAAATCAAGACAAAGCTGAATCTTGGCCCAGAGATCTTAATCCTCGTTCACAGT
CTTATAGTAGGATATGCAGGGATCAGTCAGGCAGTAGCTCTTCTTATGTCTCCATCAGGGAGTGGAGTCAAAGCTTTTCA
GGAGTCGAGGAAAATCTCACAGAGTTCAAAGGTCTGGGTCTAAAAGCACAACATCAATTTCCAGGCCAGGACTTACCCAC
ATTCCCAAAGTCAAAGCAGCAAAAGATCCAGTGACAGAAGAACCCATAGTAGAACCTGGAATAGAGATGGACATAAAATC
AGAGATGAGAAGAAAAGGATAAAGGCAGGGGTGAAGCATTACGCATCAAATGTGGGGAACCTCGAAACATCAAAGCTGGA
TGACAACACCTGTCACCAGCTGAATAGACCAAAGCCTGACTACAACTT

Alignment

ORF - retro_cpor_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.54 %
• Parental protein coverage: 54.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SDTEEESRSKRKKKHRRQSSSSSSSDSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRSSSSSS
          SDT.EES..K.KK.H.............T..RK..G.....K..SW.RDL.PRS.SY.R..R..S.SSSS
Retrocopy SDTKEES*KKSKKRHHSHLLTVIQIVKYTADRKVEG--NQDKAESWPRDLNPRSQSYSRICRDQSGSSSS

Parental  YGSRRKRSRSRS-RGRGKSYRVQRSRSKSRTRRSR-SRPRPRSHSRSSERSSHRRTRSRSRERDRRKGRD
          Y.S.R..S.S.S.R.RGKS.RVQRS.SKS.T..SR..R..P.S.S.SS.RSS.RRT...SR...R.....
Retrocopy YVSIREWSQSFS<RSRGKSHRVQRSGSKSTTSISR<ARTYPHSQSQSSKRSSDRRTH--SRTWNRDGHKI

Parental  KEKR-EKDKSKDKELHIKRGETGNIKAGLEHLPPAEQAKARLQL
          .....EKDK.....L.IK.GE..NIKAG..HL.PAE..KA.LQL
Retrocopy RDEK<EKDKGRGEALRIKCGEPRNIKAG*QHLSPAE*TKA*LQL

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	12.02 RPM
SRP017611_kidney	0.00 RPM	17.69 RPM
SRP017611_liver	0.00 RPM	14.28 RPM
SRP040447_lung	0.00 RPM	7.19 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_671 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_671 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671 ,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454, retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,