RetrogeneDB ID: retro_cpor_1127

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_49:3951196..3951798(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSCPOG00000007930
• Aliases: None
• Description: None

Sequence

>retro_cpor_1127
ATGGGAGCCATGACTGACAATGAAGTCATAAGGAAACATCTCCTTATTGATGGAGATGGTGCTGGAGACAACCGCAGAAT
TAATCTGCTAGTGAAACGTTTTATTCCATGGTGCAACTCTGGGTCCCAAGAAGAGGGATACAACCAGTACCAAAGTATGC
TGAGCACTCTATCCCAGTGTGAGTTTTCCATGGGCAAAATTTTCCTGGTGTATGATACGAATCTCAGGAAAATGGAAAAC
TATGAAAAATTTACAAAGAAATAGAATGCAGCATTGCAGGAACGCATGAAAAAATTGCTAGGTGTGTAATTCTTCAAGCA
AAACAAATACAAAAAATCGCCAAGAATATGATGATCTGGCAGAGGTGATCTAGCATCATCCAGACTGGCATAAGACCTTA
AAGGAACCAGCAGCTCTGGGGAAGAATTAGAGCATCTTTTACACATTAAAGAAAGTGTGGAAGATATGCTGAAATTATGA
CGGAAACAGTTCACATTCTTCTTAGCACCATCCATGAACTTCAGCAGACTCTGGAAAATGATGAAAAGCTCTCAGACGTA
GAAGAAGCTCGAAGAACAAGCATAGAAATGGATCCCAAGCCG

Alignment

ORF - retro_cpor_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGAVTDDEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLV
          MGA.TD.EVIRK.LLIDGDGAGD.RRINLLVK.FI.WCNSGSQEEGY.QYQ.MLSTLSQCEFSMGK..LV
Retrocopy MGAMTDNEVIRKHLLIDGDGAGDNRRINLLVKRFIPWCNSGSQEEGYNQYQSMLSTLSQCEFSMGKIFLV

Parental  YDMNLREMENYE-KIYKEIECSIAGAHEKIAECKKQILQAKRIR-KNRQEYDALAKVIQHHPDRHETLKE
          YD.NLR.MENYE.KIYKEIECSIAG.HEKIA.C...ILQAK.I..KNRQEYD.LA.VI.HHPD.H.TLKE
Retrocopy YDTNLRKMENYE<KIYKEIECSIAGTHEKIARC--VILQAKQIQ<KNRQEYDDLAEVI*HHPDWHKTLKE

Parental  LEALGK-ELEHLSHIKESVEDKLELRRKQF-HVLLSTIHELQQTLENDEKLSEVEETQETSIETDPKP
          ..ALGK.ELEHL.HIKESVED.L.L.RKQF.H.LLSTIHELQQTLENDEKLS.VEE...TSIE.DPKP
Retrocopy PAALGK<ELEHLLHIKESVEDMLKL*RKQF<HILLSTIHELQQTLENDEKLSDVEEARRTSIEMDPKP

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	11.96 RPM
SRP017611_kidney	0.00 RPM	24.08 RPM
SRP017611_liver	0.00 RPM	27.20 RPM
SRP040447_lung	0.00 RPM	18.84 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1127 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1127 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127 , retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,