RetrogeneDB ID: retro_cpor_122

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:51837491..51838253(-)
• Located in intron of: ENSCPOG00000004758

Retrocopy information

• Ensembl ID: ENSCPOG00000023350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000001392
• Aliases: None
• Description: None

Sequence

>retro_cpor_122
ATGGATGGAGGGGATGATGGTAATCTTGTCATCAAAAAGAGGTTTGTATCTGAGGCAGAATTAGAGGAACGACGCAAAAG
GCGACAAGAAGAATGGGAGAAAGTTCGAAAACCCGAAGATCCCAAAGAATGTCCAGAGGAGGTTTATGACCCACAGTCTC
TCTATGAAAGGCTACAGGAACAGAAAGACAGGAAGCAGCAGGAGTATGAGGAGCAATTCAAATTCAAAAACATGGTAAGA
GGCTTAGATGAAGATGAGACCAACTTCCTTGATGAGGTTTCTCGGCAGGAACTAATAGAAAAGCAACGAAGAGAAGAAGA
ACTGAAGGAACTAAAGGAATACAGAAGTAATCTCAATAAAGTTGGAATCTCTGCAGAAAACAAGAAGGAAGTAGAGAAGA
AACTGCCTGTGAAACCAATAGAAACCAAGAACAAGTTCTCCCAGGCGAAGCTGTTGGCAGGAGCTGTGAAGCACAAGAGC
TCAGACAGTGGCAATAGTGTGAAAAGACTGAAACCAGACCCTGACCCAGATGACAAGAGTCAAGAGGCCTCATCCTGTGT
GTCTCTTGGAAGTACCTCCCTGAGTGGCCCGTCCATTCACTGCCCCTCCACTGCTGTCTGCATTGGCATCCTCCCAGGTC
TGGGCGCCTACTCCGGAAGCAGCGACTCTGAGTCCAGCTCAGACAGTGAAGGCACCATCAATGCCACAGGGAAGATTGTC
TCCTTCATCTTCCAAACCAGCACCTTCCTTGAGGCACCCTAA

Alignment

ORF - retro_cpor_122 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPKECPEEVYDPRSLYERLQEQKDRKQQEYE
          MDGGDDGNLVIKKRFVSEAEL.ERRKRRQEEWEKVRKPEDPKECPEEVYDP.SLYERLQEQKDRKQQEYE
Retrocopy MDGGDDGNLVIKKRFVSEAELEERRKRRQEEWEKVRKPEDPKECPEEVYDPQSLYERLQEQKDRKQQEYE

Parental  EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELKELKEYRISFVLNLNKVGISAENKKEVEKKL
          EQFKFKNMVRGLDEDETNFLDEVSRQ.ELIEKQRREE...ELKE.......NLNKVGISAENKKEVEKKL
Retrocopy EQFKFKNMVRGLDEDETNFLDEVSRQ-ELIEKQRREE---ELKELK-EYRSNLNKVGISAENKKEVEKKL

Parental  PVKPIETKNKFSQAKLLAGAVKHKSSESGNSVKRLKPDPDPDDKSQEASSCVSLGSTSLSGPSIHCPSAA
          PVKPIETKNKFSQAKLLAGAVKHKSS.SGNSVKRLKPDPDPDDKSQEASSCVSLGSTSLSGPSIHCPS.A
Retrocopy PVKPIETKNKFSQAKLLAGAVKHKSSDSGNSVKRLKPDPDPDDKSQEASSCVSLGSTSLSGPSIHCPSTA

Parental  VCIGILPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLEAP
          VCIGILPGLGAYSGSSDSESSSDSEGTINATGKIVS.IF.T.TFLEAP
Retrocopy VCIGILPGLGAYSGSSDSESSSDSEGTINATGKIVSFIFQTSTFLEAP

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	2.59 RPM	20.71 RPM
SRP017611_kidney	2.93 RPM	25.65 RPM
SRP017611_liver	0.91 RPM	10.10 RPM
SRP040447_lung	0.81 RPM	14.91 RPM
SRP040447_skeletal_muscle	0.89 RPM	10.65 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_122 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_122 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122 ,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,