RetrogeneDB ID: retro_cpor_1399

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:30527782..30528061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSCPOG00000012407
• Aliases: None
• Description: None

Sequence

>retro_cpor_1399
AAAAGAAAGGCTTAAGAGAAGCCAGAGGGCAAAGATGGACCCAAAGTAACTAAACAAGAACCCACAAGACGGTCTGCCAG
ATTATCCACAAAACCTGCTCCCCTAGAACCTGAACCTAAAGCAAGAAAAGCATTTACCTAGAACAAACCTGGAACAAAGA
TCAACAGAGGAGCTAAAAAGAGGAAGAAATAATAGCGGGAAGCTGGAAAAGAAGGTACTACACCATCTGAAAATGGTGAA
AAGGTACAGAAAACTGAATCTGTAGATAATGAGGGAGAA

Alignment

ORF - retro_cpor_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.07 %
• Parental protein coverage: 97.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKQSSENTEGKEGSKVTKQEPTRRSARLSTKPAPPKPEPKPRKTAIKKEPGTKINRGAKGKKEEKQEAGK
          K....E..EGK.G.KVTKQEPTRRSARLSTKPAP..PEPK.RK......PGTKINRGAK..K....EAGK
Retrocopy KRKA*EKPEGKDGPKVTKQEPTRRSARLSTKPAPLEPEPKARKAFT*NKPGTKINRGAKKRKK**REAGK

Parental  EGTTPSENGETKAEEAQKTESVDNKGE
          EGTTPSENGE......QKTESVDN.GE
Retrocopy EGTTPSENGE----KVQKTESVDNEGE

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	17.77 RPM
SRP017611_kidney	0.00 RPM	18.22 RPM
SRP017611_liver	0.00 RPM	8.79 RPM
SRP040447_lung	0.00 RPM	22.35 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1399 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1399 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399 , retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,