RetrogeneDB ID: retro_cpor_1073

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_44:3585014..3585749(+)
• Located in intron of: ENSCPOG00000000258

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA3
• Ensembl ID: ENSCPOG00000012334
• Aliases: None
• Description: cell division cycle associated 3 [Source:HGNC Symbol;Acc:14624]

Sequence

>retro_cpor_1073
GTAGCGGACCCTCGCTTGCCTAGTGCTGGCATCCAGCGCACTCCTATCCAGGTAGAGAGCTCTCCACAAACAAGCCTGCC
AGCCAGAGAAGAGCTAGAGGATCCTAAGCAGGCCCAGGACTCAGAAGATCCTCGCTCTCCTACCCTTGGCATTGCATGGA
CACCTATAAAGACCTGCAGTGTAGGCTCTGAGAATCCACTGGTGAAACAACTGAGTGAAGTATTTGAGACTGAAGCCTCA
AAATCAGATCTTTCCTCAGAGTCCATTCTGGCCCTGGGAGCAATTTTGTCTTCTAAACTGGACTTGTCTGTGGATACTGA
GTTAATCCTGCAGGACCAGACAAAACCTTGGAACCAGACCAAGTTCCCCTCTAAACAGATGTTGTCCAAGGAGGAAGCTA
GACAGCCCACTGAAATCCTCGTGGCCATCCAGAGCTCAGACAAGCCTTCAAGAGACCTTGAGACTCCCCAATCTTCAGGT
TCTAAGCATAATTGACGGAAACAAAACAGCAAGGTACTAGGCAGGTCTCCCCTCACCATCCTGCAAGATGACAACTCCCC
TGGGACCCTGACACCACGACAGGGTAAGCGGCCTTCTCCGCTGAGTGACAATGTTAGGGAACTAAAGGAAGGAGCCACTC
TTGGAACTGGACGACTTCTGAAAACTGGAGGGCGAGCACGGGAGCCAGTCCAGGACCATGACAAAGAAAATCAACACTTT
CCTTTGGTAGAGAGC

Alignment

ORF - retro_cpor_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 91.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VADPRSPSAGIQRTPIQVESSPQTSLPAREELEDPKQAQDSEDPRSPTLGIARTPMKTCSVDSENPLVKQ
          VADPR.PSAGIQRTPIQVESSPQTSLPAREELEDPKQAQDSEDPRSPTLGIA.TP.KTCSV.SENPLVKQ
Retrocopy VADPRLPSAGIQRTPIQVESSPQTSLPAREELEDPKQAQDSEDPRSPTLGIAWTPIKTCSVGSENPLVKQ

Parental  LSEVFETEASKSDLSSESILALGAILSSKLDLSVDTELILQDQTKPWNQTKFPSKQMLSKEEARQPTETL
          LSEVFETEASKSDLSSESILALGAILSSKLDLSVDTELILQDQTKPWNQTKFPSKQMLSKEEARQPTE.L
Retrocopy LSEVFETEASKSDLSSESILALGAILSSKLDLSVDTELILQDQTKPWNQTKFPSKQMLSKEEARQPTEIL

Parental  MAIQSSDKSSRDLETPKSSGSKHNRRKQNSKVLGRSPLTILQDDNSPGTLTPRQGKRPSPLSDNVRELKE
          .AIQSSDK.SRDLETP.SSGSKHN.RKQNSKVLGRSPLTILQDDNSPGTLTPRQGKRPSPLSDNVRELKE
Retrocopy VAIQSSDKPSRDLETPQSSGSKHN*RKQNSKVLGRSPLTILQDDNSPGTLTPRQGKRPSPLSDNVRELKE

Parental  GATLGTGQLLKTGGRAREPVQDHDKENQHFPLVES
          GATLGTG.LLKTGGRAREPVQDHDKENQHFPLVES
Retrocopy GATLGTGRLLKTGGRAREPVQDHDKENQHFPLVES

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	0.06 RPM
SRP017611_kidney	0.00 RPM	0.63 RPM
SRP017611_liver	0.00 RPM	0.52 RPM
SRP040447_lung	0.08 RPM	1.46 RPM
SRP040447_skeletal_muscle	0.01 RPM	0.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1073 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1073 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073 ,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,