RetrogeneDB ID: retro_cpor_68

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:19574632..19575535(+)
• Located in intron of: ENSCPOG00000012462

Retrocopy information

• Ensembl ID: ENSCPOG00000021778
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000012839
• Aliases: None
• Description: None

Sequence

>retro_cpor_68
GATGCGCAGCCCACAGAAGGGGAGCGGGAGATCTGGAACCAGATCAGTGCCGTGCTGCAGGACTCAGAGAGCATCCTCAC
CGACCTACAGGCCTACAAGGGCGCCGGGCCGGAGATCCGAGATGCGATTCAAAACCCCAATGACATCCAGCTTCAGGAAA
AGGCCTGGAACGCTGTGTGTCCCCTGGTAGTGAGGCTGAAGCGGTTCTACGAGTTCTCCATCCGGCTAGAGACAGCCCTG
CAGAGCCTGCTGGAGTCTCTGACCTGCCCCCCCTATACCCCAACCCAGCACCTGGAGCGGGAGCAGGCCCTGGCCAAGGA
GTTTGCGGAAATCCTGCATTTCACACTTCGATTTGATGAACTGAAGATGAGGAACCCTGCCATTCAGAATGACTTCAGCT
ACTACCGAAGAACCATAAGTCGTAATCGTATCAACAACATGCATCTAGACATTGAGAATGAAGTCAATAACGAGATGGCC
AATCGCATGTCCCTCTTCTACGCAGAAGCCACGCCCATGCTGAAAACCCTGAGCGATGCCACCATGCACTTCGTCTCTGA
GAACAAAACCCTGCCGATAGAGCACACCACGGACTGCCTCAGTACGATGACCAGCGTCTGCAAAGTCATGCTGGAGACTC
CGGAGTACAGGAGCAGGTTCACGAGTGAAGAGACGCTCATGTTCTGCATGCGGGTGATGGTAGGGGTCATCATCCTCTAC
GACCATGTGCACCCGGTGGGAGCCTTCTGCAAGACGTCCAAGATCGATATGAAGGGCTGCATAAAGGTTCTGAAGGAACA
GGCCCCGGACAGCGTGGAGGGACTACTCAACGCCCTCAGGTTCACTACAAAGCACTTGAATGATGAGACCACTTCCAAAC
AGATTCGAGCCATGCTGCAGTAG

Alignment

ORF - retro_cpor_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.71 %
• Parental protein coverage: 92.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NAQPTEGEREIWNQISAVLQDSESILTDLQAYKSAGRRSEIQAIQNPNDIQLQEKAWNAVCPLVVRLKRF
          .AQPTEGEREIWNQISAVLQDSESILTDLQAYK.AG......AIQNPNDIQLQEKAWNAVCPLVVRLKRF
Retrocopy DAQPTEGEREIWNQISAVLQDSESILTDLQAYKGAGPEIR-DAIQNPNDIQLQEKAWNAVCPLVVRLKRF

Parental  YEFSIRLETALQSLLESLTCPPYTPTQHLEREQALAKEFAEILHFTLRFDELKMRNPAIQNDFSYYRR-I
          YEFSIRLETALQSLLESLTCPPYTPTQHLEREQALAKEFAEILHFTLRFDELKMRNPAIQNDFSYYRR.I
Retrocopy YEFSIRLETALQSLLESLTCPPYTPTQHLEREQALAKEFAEILHFTLRFDELKMRNPAIQNDFSYYRRTI

Parental  SRNRINNMHLDIENEVNNEMANRMSLFYAEATPMLKTLSDATMHFVSENKTLPIEHTTDCLSTMTSVCKV
          SRNRINNMHLDIENEVNNEMANRMSLFYAEATPMLKTLSDATMHFVSENKTLPIEHTTDCLSTMTSVCKV
Retrocopy SRNRINNMHLDIENEVNNEMANRMSLFYAEATPMLKTLSDATMHFVSENKTLPIEHTTDCLSTMTSVCKV

Parental  MLETPEYRSRFTSEETLMFCMRVMVGVIILYDHVHPVGAFCKTSKIDMKGCIKVLKEQAPDSVEGLLNAL
          MLETPEYRSRFTSEETLMFCMRVMVGVIILYDHVHPVGAFCKTSKIDMKGCIKVLKEQAPDSVEGLLNAL
Retrocopy MLETPEYRSRFTSEETLMFCMRVMVGVIILYDHVHPVGAFCKTSKIDMKGCIKVLKEQAPDSVEGLLNAL

Parental  RLLSRELDPQSSTSKQIRAMLQ
          R.....L.....TSKQIRAMLQ
Retrocopy RFTTKHLNDE-TTSKQIRAMLQ

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	8.45 RPM	13.11 RPM
SRP017611_kidney	0.42 RPM	1.05 RPM
SRP017611_liver	0.30 RPM	1.26 RPM
SRP040447_lung	8.52 RPM	13.52 RPM
SRP040447_skeletal_muscle	4.85 RPM	6.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_68 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_68 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012839	1 retrocopy	retro_cpor_68 ,
Microcebus murinus	ENSMICG00000013924	1 retrocopy	retro_mmur_898,
Tarsius syrichta	ENSTSYG00000010693	4 retrocopies	retro_tsyr_1129, retro_tsyr_1823, retro_tsyr_2111, retro_tsyr_827,