RetrogeneDB ID: retro_cpor_1384

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_79:4252063..4252637(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL3
• Ensembl ID: ENSCPOG00000003970
• Aliases: None
• Description: None

Sequence

>retro_cpor_1384
GACCTAGGTGAAAGACTCTCTTGGCATGTAAAGCAAATTTTTATTGATGTACTTGAGTTACTACTCCAAGATAAAGATTT
AAAAGGGATTGGGCACCACCTGAAAAAGCCAGGGGGCTGCCACCAGGATTGCAATTATAAAAAGAAGCGAGTAAGTAAGA
TTCTAGACAAAGGAATCAGACAAGTGGTAGAAAAGTTTGAAGGGTCCAAGGAGCTGGCAGAAAGAAGCACGTTTCATTTT
TTAGAAAATGATATAGAGCAAGTCAACCAGTTGGCTGTGTTTGTGGAGGCCGCACTAGACTACCATAAACAGTGCACAGA
GATCTTGCAGGAGCTGCAGGGCAAGCTGTAGATGAAGATAATGACTGCACACCGTGTCCCCAGGTACGAGTACAAGCCAA
GACTGGTGCAGAGGAGTTCTGTAGGCTCAGTGGTTTTCTACCTCTGCAGCAAAGATGTCAGGGCCTAACCCTCCCAGCAG
CAGCCCTGCCACCATGGTCTCTATGACTTTGAGTCAGAAAAACAAAGAAAATTAAGATTTTAAAGACAAGGACATTATTA
CAGTAACTAATAGA

Alignment

ORF - retro_cpor_1384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 57.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVKDSLDINVKQTFIDPLQLL-QDKDLKEIGHHLKKLEGRRLDYDYKKKRVGKIPDEEVRQAVEKFEESK
          .....L...VKQ.FID.L.LL.QDKDLK.IGHHLKK..G...D..YKKKRV.KI.D...RQ.VEKFE.SK
Retrocopy DLGERLSWHVKQIFIDVLELLLQDKDLKGIGHHLKKPGGCHQDCNYKKKRVSKILDKGIRQVVEKFEGSK

Parental  ELAERSMFNFLENDVEQVSQLAVFVEAALDYHKQTTEILQDLQRKLQMRISAAASVLRREYKPRPVKRSP
          ELAERS.F.FLEND.EQV.QLAVFVEAALDYHKQ.TEILQ.LQ.KL.M.I..A..V.R..Y...P.....
Retrocopy ELAERSTFHFLENDIEQVNQLAVFVEAALDYHKQCTEILQELQGKL*MKIMTAHRVPR--YEYKPRLVQR

Parental  SELNGVS-STSTAKTTGSNIP-MDQPCCRGLYDFEPENQGEL-GFKEGDIITLTNQ
          S....V..STS.AK..G.N.P...QPC..GLYDFE.E.Q..L..FK..DIIT.TN.
Retrocopy SSVGSVV>STSAAKMSGPNPP<QQQPCHHGLYDFESEKQRKL>DFKDKDIITVTNR

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	28.93 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1384 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1384 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003970	1 retrocopy	retro_cpor_1384 ,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Macaca mulatta	ENSMMUG00000013669	1 retrocopy	retro_mmul_1265,