RetrogeneDB ID: retro_cpor_836

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:67841984..67842298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNJ2BP
• Ensembl ID: ENSCPOG00000023967
• Aliases: None
• Description: None

Sequence

>retro_cpor_836
ATGAACGGAAGAGTGGATTATTTGGTCACAGAGGAAGAGATCGATCTTACCAGAAGACCCTCAGGTCTGGGCTTCAACAT
CGTCGGTGGGACAGCTCAGCAGTATGTCTCTAATGACAGTGGCATCTACGTCAGCAGCATCAAAGAGAACGGGGCTGCAG
CCCAGGATGGGCGACTCCAGGAGGGTGACAGATCCTCTCGGTAAATGGCCACGACCTAAAGAACCTGCAGCACCAAGATG
CTGTAGCCCTTTTCCGAAATGCTGGCTATGCTGTGTCCCTGAGAGTGCAACACAGGTGACAGGTGCAGAATGGA

Alignment

ORF - retro_cpor_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGRVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSSIKENGAAAQDGRLQEGDK-ILSVN
          MNGRVDYLVTEEEI.LTR.PSGLGFNIVGGT.QQYVSNDSGIYVSSIKENGAAAQDGRLQEGD..ILSVN
Retrocopy MNGRVDYLVTEEEIDLTRRPSGLGFNIVGGTAQQYVSNDSGIYVSSIKENGAAAQDGRLQEGDR<ILSVN

Parental  GHDLKNLQHRDAVALFRNAGYAVSLKVQHRLLVVGG
          GHDLKNLQH.DAVALFRNAGYAVSL.VQHR..V..G
Retrocopy GHDLKNLQHQDAVALFRNAGYAVSLRVQHR*QVQNG

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	11.04 RPM
SRP017611_kidney	0.31 RPM	22.30 RPM
SRP017611_liver	0.04 RPM	21.76 RPM
SRP040447_lung	0.00 RPM	12.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.20 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_836 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_836 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
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Cavia porcellus	ENSCPOG00000023967	1 retrocopy	retro_cpor_836 ,
Gorilla gorilla	ENSGGOG00000014492	1 retrocopy	retro_ggor_1470,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Oryctolagus cuniculus	ENSOCUG00000008559	1 retrocopy	retro_ocun_885,