RetrogeneDB ID: retro_cpor_787

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:2153185..2153616(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSCPOG00000007541
• Aliases: None
• Description: None

Sequence

>retro_cpor_787
GGGAAATCCTCATTGACAATTCAGTTTGTTGAAGGCCAATTTGTTGACTCCTATGATCCAACCATAAAAACACTTTCACA
AAGTTGATCACAGTAAATGGACAAGAATATCATCTTCAGCTGGTAGATACAGCTGGGCCAGATGAATATTGTATTTTCCC
TCAGACATACTCCATAGATATTAATGGCTATATTCTTGTGTATTCTGTTACATCAATCAAAAGTTTTGAAGTGATTAAAG
TTATCCATGGCAAATTGTTGGACATAGTGGGGAAAGGGCAAATACCTATTATGTTGGTTGGGAATAAGAAAGACTTGCAT
ATGGAAACGGTGATCAGTTATGAAGAAGGGAAAGCTTTGGCAGAATTGTAGAATACAGCTTTTTCGGAATCTTCTGCTAA
AAAAAATCAGACTGTCATCGATATTTTCAAA

Alignment

ORF - retro_cpor_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKSSLTIQFVEGQFVDSYDPTIE-NTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYS
          GKSSLTIQFVEGQFVDSYDPTI..NTFTKLITVNGQEYHLQLVDTAG.DEY.IFPQTYSIDINGYILVYS
Retrocopy GKSSLTIQFVEGQFVDSYDPTIK<NTFTKLITVNGQEYHLQLVDTAGPDEYCIFPQTYSIDINGYILVYS

Parental  VTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTA
          VTSIKSFEVIKVIHGKLLD.VGK.QIPIMLVGNKKDLHME.VISYEEGKALAE..N.AF.ESSA...QT.
Retrocopy VTSIKSFEVIKVIHGKLLDIVGKGQIPIMLVGNKKDLHMETVISYEEGKALAEL*NTAFSESSAXXXQTV

Parental  VDVFR
          .D.F.
Retrocopy IDIFK

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	0.17 RPM	50.73 RPM
SRP017611_kidney	0.00 RPM	56.22 RPM
SRP017611_liver	0.00 RPM	30.64 RPM
SRP040447_lung	0.00 RPM	50.29 RPM
SRP040447_skeletal_muscle	0.01 RPM	43.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_787 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_787 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787 ,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,