RetrogeneDB ID: retro_cpor_292

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:47469830..47470826(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBFD1
• Ensembl ID: ENSCPOG00000006872
• Aliases: None
• Description: None

Sequence

>retro_cpor_292
ATCGGTAGGTTGGCTTCTTCCCGGCGGCCTCTGCGTGCGCGGTGGGTGTTGTACACAATCATCATGGCGGCTGCTGGGGC
CGGATGGTATGGAGGAGTCTGGCATGGACACGGAGGCCCAGACAGTAGTAGTCACGGAGGCGCCCCGCGGCAGCTCAACT
GCTAGGGGCCGAAGCGTCGGCGGGGGCGGCTCCCGAGGACTACTGCAACCCGTGAGACAACCTGCAGCCTGCCCCTGCCC
AGCCCCCTGGGGACTCTGCGGCCCAGGCCTAGGTCAGCAATGGCGAGGACGCAGGCGGCGGCGCGGCCAGAGAGCTGGAG
CTGGTGGACCTGCAGATCATCTGGAACAAGACCAAGTACGACGTGAAGGTTCCTCTGGACAGCACAGGTTCCGAGCTGTA
ACAGAAGATTCACTCCATTACAGGACTCCCACCTGCCATGCAAAAGGTCATGTATAAGGGGCTTGTCCCTGAAGATACCA
CGTTGAGGGAAATAAAAGTGACCAGTGGGGCCAAGATCATGGTGGTTGGCTCCACAATAAATGATGTTTTAGCAGTAAAC
ACACCCAAAGATGTTTCGCAACAGGATGCAAAGGCTGAAGAGAACAAGAAAGAGCCTCTCTGCTGGCAGAAACAACACAG
GAAAGTGTTGGATAAAGGAAAACCTGAAGATGTGATGCCTTCTGTTAAGGGTGTCCAGGGGCGCCTGCCAGCGGTACCTT
TGTCTGGCATGTACAATAAGTCTGGAGGAAAAGTGAGACTCACCTTTAAGCTAGAACAAGACCAGCTGTGGATTGGCACT
AAAGAACGGACTGAGAAATTGCCCATGGGCTCCATTAAAAAATGTGGTCAGTGAACCTCTTGAAGGACATGAGGACTACC
ACATGATGGCGTTTCAGTTGGGCCCCACGGAAGCCTCTTACTACTGGGTGTACTGGGTTCCAACTCAATATGTGGATGCA
ATCAAAGACACTGTGCTGGGCAAATGGCAGTATTTT

Alignment

ORF - retro_cpor_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 90.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSRFASSRRPLRERWVLYTIIMAAAGA-PDGMEESGMDTEAETVV-TEAPA-RQLNC-VEAEAAAGAAPE
          ..R.ASSRRPLR.RWVLYTIIM.AA...PDGMEESGMDTEA.TVV.TEAP..RQLNC...AEA.AGAAPE
Retrocopy IGRLASSRRPLRARWVLYTIIM-AAAG>PDGMEESGMDTEAQTVVVTEAPR<RQLNC<LGAEASAGAAPE

Parental  DYCDARDNLQPAPAQPPGDSAAQASVSNGEDAGGGAGRELELVDLKIIWNKTKHDVKVPLDSTGSELKQK
          DYC...DNLQPAPAQPPGDSAAQA.VSNGEDAGGGA.RELELVDL.IIWNKTK.DVKVPLDSTGSEL.QK
Retrocopy DYCNP*DNLQPAPAQPPGDSAAQA*VSNGEDAGGGAARELELVDLQIIWNKTKYDVKVPLDSTGSEL*QK

Parental  IHSITGLPPAMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDASQQDAKAEENKKEP
          IHSITGLPPAMQKVMYKGLVPED.TLREIKVTSGAKIMVVGSTINDVLAVNTPKD.SQQDAKAEENKKEP
Retrocopy IHSITGLPPAMQKVMYKGLVPEDTTLREIKVTSGAKIMVVGSTINDVLAVNTPKDVSQQDAKAEENKKEP

Parental  LCRQKQHRKVLDKGKPEDVMPSVKGVQERLPAVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPM
          LC.QKQHRKVLDKGKPEDVMPSVKGVQ.RLPAVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPM
Retrocopy LCWQKQHRKVLDKGKPEDVMPSVKGVQGRLPAVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPM

Parental  GSIK-NVVSEPIEGHEDYHMMAFQLGPTEASYYWVYWVPTQYVDAIKDTVLGKWQYF
          GSIK.NVVSEP.EGHEDYHMMAFQLGPTEASYYWVYWVPTQYVDAIKDTVLGKWQYF
Retrocopy GSIK>NVVSEPLEGHEDYHMMAFQLGPTEASYYWVYWVPTQYVDAIKDTVLGKWQYF

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	0.06 RPM	16.05 RPM
SRP017611_kidney	0.21 RPM	27.53 RPM
SRP017611_liver	0.04 RPM	17.50 RPM
SRP040447_lung	0.05 RPM	17.18 RPM
SRP040447_skeletal_muscle	0.01 RPM	22.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_292 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_292 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372,
Cavia porcellus	ENSCPOG00000006872	2 retrocopies	retro_cpor_292 , retro_cpor_635,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,