RetrogeneDB ID: retro_cpor_1213

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_57:2393959..2394410(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5A
• Ensembl ID: ENSCPOG00000005322
• Aliases: None
• Description: None

Sequence

>retro_cpor_1213
CTTGATGACATAACAGTGAAGTTTGAAATATGAAAGACAGCTCACCAAGAATGATACCACAGCCAGCACCAATGGACCAC
AGAGGGCACAAGTGGTCACTGCTGTATATGATATCATGAATGAGCCTTTTGCAAGAGTGACAAACTGCTTTAAAGAACTT
CAGAGGTAAGCAAGCTCTAGCACTGTATTATCTGTATCAGGATACAAGGCTGATCTAGCAAATAAAAGAGCTGTAGATTC
CCAAAAAGTACAGTCCTTTGCAGATGACAGCAGTTTATTATTTGTGGAAACATCAGCTAAAATATCAATGAATGTAAATG
AAATATTCATTGTAATAGCTAAAAAGTTGCCAAAGAATGAACCACAGAATCCAAGAGCAAATTCTGCTAGAGGAAGTGGG
GTAGACCTTACTGAGCCTACACAACTAACCAGGAGTCAGTTTTGCAGTAAC

Alignment

ORF - retro_cpor_1213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.08 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDDTTVKFEIWDTAGQERYHSL-APMYYRG-AQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALS
          LDD.TVKFEI..TA.QE.YHS..APM..RG.AQ....VYDI.NE..FAR..N..KELQR.AS...V...S
Retrocopy LDDITVKFEI*KTAHQE*YHSQ<APMDHRG<AQVVTAVYDIMNEP-FARVTNCFKELQR*ASSSTVLSVS

Parental  GNKADLANKRAVDFQEAQSYAEDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSARGRGVDL
          G.KADLANKRAVD.Q..QS.A.D.SLLF.ETSAK.SMNVNEIF..IAKKLPKNEPQNP.ANSARG.GVDL
Retrocopy GYKADLANKRAVDSQKVQSFADDSSLLFVETSAKISMNVNEIFIVIAKKLPKNEPQNPRANSARGSGVDL

Parental  TEPTQPTRSQCCSN
          TEPTQ.TRSQ.CSN
Retrocopy TEPTQLTRSQFCSN

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	35.32 RPM
SRP017611_kidney	0.00 RPM	30.46 RPM
SRP017611_liver	0.00 RPM	23.11 RPM
SRP040447_lung	0.00 RPM	21.14 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1213 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1213 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213 , retro_cpor_219,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,