RetrogeneDB ID: retro_cpor_1303

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_67:6879567..6880152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004786
• Aliases: None
• Description: None

Sequence

>retro_cpor_1303
GTGTCAAAGGGAGGCAGTGATGTTGACATTTTTACTCCAAGCAAACCCAGCATCATGAAAGTCTTCTTATGTGTTATGAT
GCTATAGTTTTTGGAAAAAAGTTTTGAATTTGAAAAATGGGCAGAAACAAAAGGACTCATTGTCCATAGGGCCAAATGAC
TTTCTCATTAGGATCTGATCTGAATGCTGGGGGAGAATCAGAGGATGCAATGCGCTTATCCGTGTTTATGTAAAACACTG
TAGCAGGAAATATTAGACCTTCTTTAACATAAGTTGTGCTACCTCAAGGTCAGGTATTGAGAGGAGGAGCAGAATTTACT
ACACTGTATGATTTCAGGGTAATGATTTCAGATAGTGAGATGAGATTTGTCCTCAAAGATATGGGTACAATTCCAAGTTG
AAATAGTGCTACCAGTTTGGCTCAAATCATTGCCAGTAGACTAGCTCACACAGTATTAAGTTTGTCTCTCAAACTGAGTT
CAGAGAAGCTTTAAATATAGGAATGGCTCAAGAGGTCTTATAGTATTTAGATGAAACTAAATCTCTAGCTGAGGTACAGG
GTAGTTAATAGAATTTGTAAATGGC

Alignment

ORF - retro_cpor_1303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.5 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQKDDSGIGILTLNNPSKMNAFSGVMMLQLLEKVIELENWTAGKGVIVRGAK-NTFSSGSDLNAVKALAT
          ..K..S...I.T...PS.M..F..VMML..LEK..E.E.W...KG.IV..AK..TFS.GSDLN...A...
Retrocopy VSKGGSDVDIFTPSKPSIMKVFLCVMML*FLEKSFEFEKWAETKGLIVHRAK<MTFSLGSDLN---AGGE

Parental  PEDGMALCMFMQNTLTRFTRLPLISVALVQGRALGGGAELTTACDFRLMTPESEIRFVHKEMGIIPSWGG
          .ED.M.L..FM.NT.....R..L..V.L.QG..L.GGAE.TT..DFR.M...SE.RFV.K.MG.IPS...
Retrocopy SEDAMRLSVFM*NTVAGNIRPSLT*VVLPQGQVLRGGAEFTTLYDFRVMISDSEMRFVLKDMGTIPS*NS

Parental  ASRLVEIIGSRAALKVLGGALKLDPTK-ALSIGMADEILQSSDETKSVEEAQAW-LAQFVNG
          A..L..II.SR.A..VL...LKL...K.AL.IGMA.E.L...DETKS..E.Q...L..FVNG
Retrocopy ATSLAQIIASRLAHTVLSLSLKLSSEK<ALNIGMAQEVL*YLDETKSLAEVQGS<LIEFVNG

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	10.24 RPM
SRP017611_kidney	0.00 RPM	24.50 RPM
SRP017611_liver	0.00 RPM	12.75 RPM
SRP040447_lung	0.00 RPM	22.80 RPM
SRP040447_skeletal_muscle	0.01 RPM	8.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1303 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1303 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001069	1 retrocopy	retro_cfam_2182,
Cavia porcellus	ENSCPOG00000004786	1 retrocopy	retro_cpor_1303 ,
Echinops telfairi	ENSETEG00000006454	2 retrocopies	retro_etel_2049, retro_etel_564,
Mustela putorius furo	ENSMPUG00000014606	1 retrocopy	retro_mputfur_14,
Sorex araneus	ENSSARG00000011144	2 retrocopies	retro_sara_149, retro_sara_255,