RetrogeneDB ID: retro_cpor_950

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_36:19146984..19147326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSCPOG00000003553
• Aliases: None
• Description: None

Sequence

>retro_cpor_950
ATGTCTTCTAAAAGAAGGCTGTTCTTCCTCACCGAGCTCAAATTCAACGCCAATGAGCACACCCTGGAGACTACATCATC
AGCTTTGGGCTCGTTACTGTGGTGGTTGTTGTCAAGGACCAGGAAACTCAGAGATGTCAGAGTTTTGGCTTCATCGCCTT
CACCAATTCAGAATACACCTCAGATGCCATAAGAGTCATGAACGGAGAGTCCCTGGATGGTCACCAGATCCGGGCGGACA
TGTAGGCTAATCTTCCCAGGGCACCAGAGAGGGAGTGCCTGTGAGACCCATGAACGTCTCTAGAGCTACTCTAGAGATGA
TGGGGACCAGAGCTGTGGAAGT

Alignment

ORF - retro_cpor_950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.93 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFSTDEQALE-DHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNG
          MSS.....F...L.F...E..LE.D...SFG....VVVVKD.ETQR...FGFI.FTN.E..SDA.R.MNG
Retrocopy MSSKRRLFFLTELKFNANEHTLE<DYIISFGLVTVVVVVKDQETQRCQSFGFIAFTNSEYTSDAIRVMNG

Parental  ESLDGRQIRVD-HAGKSARGTR-GGGAFGAHGRGRSYSRGGGDQGYGS
          ESLDG.QIR.D.H.G.S..GTR..G.A...H.R..SYSR..GDQ..GS
Retrocopy ESLDGHQIRAD<HVG*SSQGTR<RGSACETHERL*SYSRDDGDQSCGS

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	28.87 RPM
SRP017611_kidney	0.00 RPM	37.58 RPM
SRP017611_liver	0.00 RPM	14.84 RPM
SRP040447_lung	0.00 RPM	51.07 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_950 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_950 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 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950 ,
Cavia porcellus	ENSCPOG00000006313	1 retrocopy	retro_cpor_162,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,