RetrogeneDB ID: retro_cpor_1171

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:390212..390480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013476
• Aliases: None
• Description: None

Sequence

>retro_cpor_1171
CGGGGGGCCGTTAGACCTTGGCCTTTAGTCCTAGCCCACACTGCCTTTTCACTGCCCTGCCCTACTCTTATGGGATTCAC
AGAAAAAGAGGACGAAATCGCTGCCAATAGAGTTTGTCAGCCACGTCTGGCCTTTGCGGTTACCTGCTATGGTTTGGTTT
CATACTGCAGGAGAGTTTACTGACACTTCAGAACTGAAAAAGACACCTGACGCCTTCAGGCACCACCCATGCTTGTAAGT
ATTTAATCATCGTGGTCAAGTACTCTTT

Alignment

ORF - retro_cpor_1171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 72.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIV-HIAGEFKDMDATSE
          .G.V......LAH.AFS.......M..TEKEDE......V.Q..LAFAVTCYG.V.H.AGEF.D...TSE
Retrocopy RGAVRPWPLVLAHTAFSLPCP-TLMGFTEKEDE-IAANRVCQPRLAFAVTCYGLV>HTAGEFTD---TSE

Parental  LKNKTFDTLRNHPSFYVFNHRGRVLF
          LK.KT.D..R.HP...VFNHRG.VLF
Retrocopy LK-KTPDAFRHHPCL*VFNHRGQVLF

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	4.89 RPM
SRP017611_kidney	0.00 RPM	4.71 RPM
SRP017611_liver	0.00 RPM	6.40 RPM
SRP040447_lung	0.13 RPM	5.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1171 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1171 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171 , retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,