RetrogeneDB ID: retro_cpor_92

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:15924808..15925336(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008137
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSCPOG00000025074
• Aliases: None
• Description: None

Sequence

>retro_cpor_92
ATGGGGAAGGTGCTATCTAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGTCTGGACGCGGCCGGCAAGAC
AACCATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATCCCCACCGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAATGTCAAGTTCAACGTGTGGGATGTAGGCGGCCAGGACAAGATCCGACCGCTCTGGCGGCATTACTACACCGGG
ACCCAGGGTCTGATCTTCGTCGTGGACTGCGCCGACCGCGACCGCATCGACGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCATG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCGGGGGAC
GGACTTTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCTTAA

Alignment

ORF - retro_cpor_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
Retrocopy GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
          PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
Retrocopy PLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL

Parental  HSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
          ...R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy TRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	13.29 RPM	230.76 RPM
SRP017611_kidney	31.41 RPM	29.52 RPM
SRP017611_liver	16.71 RPM	16.45 RPM
SRP040447_lung	52.16 RPM	43.63 RPM
SRP040447_skeletal_muscle	19.33 RPM	8.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_92 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_92 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 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92 ,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,