RetrogeneDB ID: retro_cpor_635

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:32753704..32754485(-)
• Located in intron of: ENSCPOG00000023184

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_635
GGCATGGAGGAGTCTCGCACGGACACTGAGGCTGAGATGTGGTCAGCGAGGCACCTGCGTGGCTGCTCAGCTGCATAGAG
GCTGAAGTTGCAGTGGATGCAACATCTGAGGATTCCTACAATATGCTAGGCAGCCTGCAGCCAGCCCTGCCCAGCCTGCT
GGGGACTCTGCAGCCTGGGCCCTGGTCATCAACTGTGAGGATGTGGGTATGGCTCAGGCAGAGAGCTGGAGCTGTGGACC
TGAAAAGCATTTGGAACAAGACCAAGTGTAATGTGAAGGTTCTTCTTGACAGCACAGGCTCTGAGCTAAAATAAAAGATT
CACTCCTTTACAGGATTCCTGCCTGCCATAAAAAAGACCATGTATAAAAGGCTCCTCCCTGAAGATACGATGTTAAGGGA
AAGAAAAGTGACCAGTGGAGCCAAGATCATGGTGGTTGGCGCCATGATAAATGATGTTTTAGCAGCATACACACCCAAAG
ATGCTTTGCAACGGGATGCAAAGGCTGGAGAGAACAAGAAGGAGCTTCTCTGCAGGCAGACACAACACAGGAGAGTGTTG
GATAAAGGAAAACTTGAAGATGTGACCTCTTCTGTGAAGGTGTCCAGGAGCGCCTGCCAGGGATTGCTTTGTCGGGCATA
TACAGTAAGTCTGGAGAAGAGAGACTCATTTTTAAGTCTAGAGCAAGACCAGCTGTGGATTGGTGCTACAGGTGGACTGA
CAAGCTACCCATGGGCTCCAGTAAAGATGTGGCCACTGAACCTATGGAAGGACACAAAGAA

Alignment

ORF - retro_cpor_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.52 %
• Parental protein coverage: 71.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GMEESGMDTEAET-VVTEAPARQLNCVEAEAAAGAAPEDYCDARDNLQPA-PAQPPGDSAAQASVSNGED
          GMEES..DTEAE..VV.EAPA..L.C.EAE.A..A..ED.......LQPA.PAQP.GDSAA.A.V.N.ED
Retrocopy GMEESRTDTEAEM<VVSEAPAWLLSCIEAEVAVDATSEDSYNMLGSLQPA<PAQPAGDSAAWALVINCED

Parental  AGG-GAGRELEL-VDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTLREI
          .G..G.GRELEL.VDLK.IWNKTK..VKV.LDSTGSELK.KIHS.TG..PA..K.MYK.L.PED..LRE.
Retrocopy VGM<GSGRELEL<VDLKSIWNKTKCNVKVLLDSTGSELK*KIHSFTGFLPAIKKTMYKRLLPEDTMLRER

Parental  KVTSGAKIMVVGSTINDVLAVNTPKDASQQDAKAEENKKEPLCRQKQHRKVLDKGKPEDVMPSVK-GVQE
          KVTSGAKIMVVG..INDVLA..TPKDA.Q.DAKA.ENKKE.LCRQ.QHR.VLDKGK.EDV..SVK.GVQE
Retrocopy KVTSGAKIMVVGAMINDVLAAYTPKDALQRDAKAGENKKELLCRQTQHRRVLDKGKLEDVTSSVK<GVQE

Parental  RLPAVPLSGMYNKSGGKVRLTFK-LEQDQLWIGTK-ERTEKLPMGSIKNVVSEPIEGHED
          RLP...LSG.Y.KS.G..RL.FK.LEQDQLWIG.....T.KLPMGS.K.V..EP.EGH..
Retrocopy RLPGIALSGIYSKS-GEERLIFK>LEQDQLWIGAT<RWTDKLPMGSSKDVATEPMEGHKE

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	0.00 RPM	27.53 RPM
SRP017611_liver	0.00 RPM	17.50 RPM
SRP040447_lung	0.00 RPM	17.18 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_635 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_635 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,