RetrogeneDB ID: retro_cpor_772

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:25923675..25924129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF58
• Ensembl ID: ENSCPOG00000009679
• Aliases: None
• Description: None

Sequence

>retro_cpor_772
AAGTCTTCAGCTTTCAGAGACAATGACCTCAGATCTAGCGATTGGAAGGAAGCAGACTTGGGCAGTCAAGAGAGAAAACT
AAAGTTCTTCAGACGTTCCTCAGGGTGCAGGAAAAAAGGAACACACGAGTCATCTTGTTATAGGAGATCACAAATCAACA
TCACATTTCCGTCCAGGAGAAGAAGCCAAGAAAATTAATGAAAAATTGGAGTCTCAGTATCAGCACTGTGTACAGTAAAT
AGTCAGGAAGCATCGATGGCGCTGTGAACTTGGCTTCAGTGAGGTAGACCATGATGGAGGAGGTGATGCGGCTACAGATG
ATGATGATGATGATGATGATGATGATGATGATGATGATGAAGACAACAACCACGAGGATGACTCACCTGACCCTGAAAGT
CCGAATGAGTCTGAAACTGATACAGGGTCAGAAAAGGAAGACTCTACCAACAAA

Alignment

ORF - retro_cpor_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.32 %
• Parental protein coverage: 84.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRSASPDDDLGSSNWEAADLGS-EERKQKFLRL-MGAGKKEHTGRLVIGDHKSTSHFRTGEEDKKINEEL
          K.SA..D.DL.SS.W..ADLGS.E.....F.R...GAGKKEHT..LVIGDHKSTSHFR.GEE.KKINE.L
Retrocopy KSSAFRDNDLRSSDWKEADLGSQERKLKFFRRS>QGAGKKEHTSHLVIGDHKSTSHFRPGEEAKKINEKL

Parental  ESQYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAADDDDDDDSPDPESPDDSESDSESEKEESADEL
          ESQYQ...........R..C.LGFSEV.DHDG.GD.A................D......S...ES..E.
Retrocopy ESQYQHCV-Q*IVRKHRWRCELGFSEV-DHDGGGDAATXXXXXXXXXXXXXXXDNNHEDDSPDPESPNES

Parental  QATEHPDEVEDPKNK
          ..T....E.ED..NK
Retrocopy E-TDTGSEKEDSTNK

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	0.06 RPM	28.30 RPM
SRP017611_kidney	0.00 RPM	34.55 RPM
SRP017611_liver	0.00 RPM	30.21 RPM
SRP040447_lung	0.00 RPM	34.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	30.76 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_772 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_772 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772 ,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,