RetrogeneDB ID: retro_cpor_231

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_103:3264073..3264607(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSCPOG00000025788
• Aliases: None
• Description: None

Sequence

>retro_cpor_231
GAAGATGCAGTTCGCTGGGAGCCACCCCTGAGCAGAAGCTCTTGTCCTGGAGACTCCTGACCAAGACCAACAGGATGCCT
GCTGGGCAGAGCGACCGTTTCCTGCCAACCCTGCTCACTAGTATACATCCTGAGGACTCTAGAGCAGACCCAGGGAATCA
GACCATGATCACTTTCACCAGGATTATCAACCGTGTCTGGCTGATGGTGGTGGAGGAACAATGTGTTTGTTTACTGTCTG
AACTGGGACAACAGTGGCTGGAATGAAATCCCTGGGAAGCCTGGGTCTCCTCTATTCTATTTGGTTTCTCCAGAGCTGTC
CAGGAATTTGTCCTCACCTAGTTCCAAAGTAATGTGACCAAGGCTATGAAGGGTTTTGAATACATTTTCACCAATTTGCA
AGGCAAGGCCCCTCTTAAACACTTATGGAGACAGTCAAGAAGCCAAGGAGAAAGCAAAGGAGAGCACTGGCAGGTACAAG
GAGGCCAAGGACCTTGGCAACAAGGCTGCCACCAAGCAGCAGTAGAGACAACAG

Alignment

ORF - retro_cpor_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 82.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EDIVHRE-VTPDQKLLSRRLLTKTNRMPR-WAERLFPANVAH-SVYIL-EDSIVDPQNQTMTTFTWNINH
          ED.V..E..TP.QKLLS.RLLTKTNRMP..WAER.FPAN.AH..VYIL.EDS..DP.NQTM.TFT..IN.
Retrocopy EDAVRWE<ATPEQKLLSWRLLTKTNRMPA<WAERPFPANPAH<LVYIL<EDSRADPGNQTMITFTRIINR

Parental  ARLMVVEERCVYCVNSDNSGWTEIRR-EAWVSSSLFGVSRAVQEFGLARFKSNVTKTMKGFEYILAKLQG
          ..LMVVEE.CV.........W.E....EAWVSS.LFG.SRAVQEF.L..F.SNVTK.MKGFEYI...LQG
Retrocopy VWLMVVEEQCVCLLSELGQQWLE*NPWEAWVSSILFGFSRAVQEFVLT*FQSNVTKAMKGFEYIFTNLQG

Parental  EAPSK-TLVETAK-EAKEKAKETALAATEKAKDLANKAATKQQQQQQ
          .AP.K.TL.ET.K.EAKEKAKE........AKDL.NKAATKQQ..QQ
Retrocopy KAPLK<TLMETVK<EAKEKAKEST-GRYKEAKDLGNKAATKQQ*RQQ

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	22.49 RPM
SRP017611_kidney	1.15 RPM	51.92 RPM
SRP017611_liver	0.00 RPM	26.25 RPM
SRP040447_lung	0.00 RPM	52.26 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_231 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_231 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 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231 ,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236, retro_mmus_2394, retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178, retro_rnor_2305, retro_rnor_637, retro_rnor_995,