RetrogeneDB ID: retro_cpor_1260

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_60:3027061..3027337(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000001818
• Aliases: None
• Description: None

Sequence

>retro_cpor_1260
AAGAACACTAAGTCAAGCAGAACAAGCACAAAGAGGTGAGAGGCCATTACTGCAGCAACCTGCCTGACAGGAGCTTTGGA
GGACCACCTCAGTGTGGGTGCGGTCCAGCCTACATGTACCAAAGAAAGTTGGACCATGAACTGAAGACCCTGCACGTCCA
AGCTGCCCAGTTTACCATGCAGACAGCCCAGTGGATTAGGAAGGTGGAGAACTTCAACTAGGTGCTAAGGGAATTGGGGA
TGTGGAGAATTGGCTAGGAGCATTGAGTTGGGCATG

Alignment

ORF - retro_cpor_1260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.71 %
• Parental protein coverage: 74.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QNERKELQEKRRREAITAATCLTEALVDHLNVGVAQ-AYMNQRKLDHEVKTLQVQAAQFAKQTGQWIGMV
          .N.........R.EAITAATCLT.AL.DHL.VG..Q.AYM.QRKLDHE.KTL.VQAAQF..QT.QWI..V
Retrocopy KNTKSSRTSTKR*EAITAATCLTGALEDHLSVGAVQ<AYMYQRKLDHELKTLHVQAAQFTMQTAQWIRKV

Parental  ENFNQALKE-IGDVENW-ARSIELDM
          ENFN..L.E.IGDVENW.ARSIEL.M
Retrocopy ENFN*VLRE<IGDVENW<ARSIELGM

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	13.86 RPM
SRP017611_kidney	0.00 RPM	32.24 RPM
SRP017611_liver	0.00 RPM	17.89 RPM
SRP040447_lung	0.00 RPM	27.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	31.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1260 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1260 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260 , retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,