RetrogeneDB ID: retro_cpor_618

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:8528911..8529515(+)
• 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_618
AGAGTTCAGAGGTCGAGGTCTAAAAGCAGCACAAGACGGTCCAGGTCAAGACCTTGTCCACTTTCCCATGGTTGAAGCAG
TGAAAGACCCAGTCACAGAACCCACAGCAGGTCCCAGGATAGAGATTGACATAAAGGCAGAGATAAAGAGAAAAGAGAAA
AAGATAAAGGCAAGGACAAAGAATTACACATCAAATGGGGAAATGGAAACATCAAAGCTGGATTAGGACATCCGCCAGCA
GCCGAACAGACCAAAGCCAGACTGCATCTAGCTCTTGAGGCCGCTGCAAAAGCTGATGAAGCACTGAAGGGCAAAGAAAG
AAATGAGGAGGGAGCTGAGAAAAGAAAGGAGGAAGACCAGGCCACCCTGGCAGGCAAGTACAAAGAGGAACAGAAATCGG
AGCTGTTGGAAGTGATTCTGTCCCTCAGCAGATGTTCAGACCAAGTAAAGAAGTCAAAAAGTCGGTGGAACCTAGTGAGG
TGAGACATACAACTTCAGCATCAGGACTGGCTTCTGCAGGTGCTGACCCACCAGTGTTGAGAAAGAAACAGACCCTAGGA
GCATCCCTATCGCTATCATGTACCAAGATGACGATTCTCTGGCT

Alignment

ORF - retro_cpor_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 61.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRERDRRKGRDKEKREKDKSKDKELHIKRGET
          RVQRSRSKS.TRRSRSRP.P.SH..SSER.SHR.T.SRS..RD..KGRDKEKREKDK.KDKELHIK.G..
Retrocopy RVQRSRSKSSTRRSRSRPCPLSHG*SSERPSHR-THSRSQDRD*HKGRDKEKREKDKGKDKELHIKWGN-

Parental  GNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEEEAKRRKEEDQATLI-EQVKRVKEIEAIE
          GNIKAGL.H.P.AEQ.KARL.L.LEAAAKADEALK.KERNEE.A..RKEEDQATL...QV.R..EI.A..
Retrocopy GNIKAGLGHPPAAEQTKARLHLALEAAAKADEALKGKERNEEGAEKRKEEDQATLA<RQVQRGTEIGAVG

Parental  SDSFVQQTFRSSKEVKKLVEPSEVKHTTSASGPASVVAEPP-SVEKEIDPSSIPTTIKYQDDNSLA
          SDS..QQ.FR.SKEVKK.VEPSEV.HTTSASG.AS..A.PP.SVEKE.DP.SIP..I.YQDD.SLA
Retrocopy SDSVPQQMFRPSKEVKKSVEPSEVRHTTSASGLASAGADPP<SVEKETDPRSIPIAIMYQDDDSLA

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	0.23 RPM	12.02 RPM
SRP017611_kidney	0.21 RPM	17.69 RPM
SRP017611_liver	0.04 RPM	14.28 RPM
SRP040447_lung	0.08 RPM	7.19 RPM
SRP040447_skeletal_muscle	0.08 RPM	6.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_618 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_618 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,