RetrogeneDB ID: retro_cpor_232

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_103:1646703..1646922(-)
• Located in intron of: ENSCPOG00000013291

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL1
• Ensembl ID: ENSCPOG00000006718
• Aliases: None
• Description: Gamma-aminobutyric acid receptor-associated protein-like 1 [Source:UniProtKB/Swiss-Prot;Acc:P60518]

Sequence

>retro_cpor_232
GTACCTGATCTGAACAAGGGGAAGTACCTAGTGCCTTCTGACATGGTTGGCCAGTTTTACTTCTTAATCTGGAAGAAACT
GATTAAGAACACCCAAAGACCCCTTATTCGCTGTCAACATCCCTCCCATTAGTGTTACTTGGGCCACCCATACGAGAACA
CCCCATGAGGAAGACTACTTTCTGTCTGTGGCCCAACAGGGATGAGAGTCTATGGGAAG

Alignment

ORF - retro_cpor_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.43 %
• Parental protein coverage: 65.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPDLDKRKYLVPSDLTVGQFYFLIRKRIHLR-PEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAY
          VPDL.K.KYLVPSD..VGQFYFLI.K......P.D.LF......IPP.S.T........HEEDYFL.VA.
Retrocopy VPDLNKGKYLVPSDM-VGQFYFLIWKKLIKN>PKDPLFAV---NIPPISVTWATHTRTPHEEDYFLSVAQ

Parental  -SDESVYGK
          .....VYGK
Retrocopy <TGMRVYGK

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	351.66 RPM
SRP017611_kidney	0.00 RPM	432.78 RPM
SRP017611_liver	0.00 RPM	313.78 RPM
SRP040447_lung	0.00 RPM	158.87 RPM
SRP040447_skeletal_muscle	0.01 RPM	32.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_232 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_232 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006718	1 retrocopy	retro_cpor_232 ,
Cavia porcellus	ENSCPOG00000023922	1 retrocopy	retro_cpor_394,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Tarsius syrichta	ENSTSYG00000005307	19 retrocopies	retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234, retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,