RetrogeneDB ID: retro_cpor_186

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:6631565..6631900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0101
• Ensembl ID: ENSCPOG00000006482
• Aliases: None
• Description: None

Sequence

>retro_cpor_186
ATGGTGCAGACTAAAGCAGACAGCGTACTGGGCAGTTACAGGAAAACAGTGACCTCTGGAGCCCTCAAGAAGGCGGCTGG
GTCCCTCCACCTCTGCCACGAATTCCATGTTGCTTTTGTCCTCAAGGAAAGATGAAAATAAATATTCAGGAGGGAATCCA
GTTTGTATATGTTCAACTCCCGAGTGTCAAAAAAGAATTGAAGAATTCTTCAGGTTTTCCCTAAAGATTCTGAAAAAGAG
AATTGAATTCCTGAAGACCCATAAGTATTGGCTTAGGAAAAACAAAGAGAAAATCCAGTCCTTTGTAACCTAATCACAGT
GATGAAGAAAAGGAT

Alignment

ORF - retro_cpor_186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVRTKADSVPGTYRKVVASRAPRKV-LGPSTSATNSRAFSSSRKAENKYSGGNPVCVRPTPKWQKGIGEF
          MV.TKADSV.G.YRK.V.S.A..K..LGPSTSATNS....SSRK.ENKYSGGNPVC...TP..QK.I.EF
Retrocopy MVQTKADSVLGSYRKTVTSGALKKA>LGPSTSATNSMLLLSSRKDENKYSGGNPVCICSTPECQKRIEEF

Parental  FRLS-PKDSEKENRIPEE-PGSSGLGKTNRKARPLQPDHSDDEKE
          FR.S.PKDSEKEN.IPE..P.S.GLGKT.RK..PL.P.HSD.EK.
Retrocopy FRFS<PKDSEKEN*IPED<PISIGLGKTKRKSSPL*PNHSDEEKD

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	0.29 RPM
SRP017611_kidney	0.00 RPM	0.31 RPM
SRP017611_liver	0.00 RPM	1.04 RPM
SRP040447_lung	0.00 RPM	2.14 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.28 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_186 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_186 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010763	2 retrocopies	retro_chof_1104, retro_chof_892,
Cavia porcellus	ENSCPOG00000006482	3 retrocopies	retro_cpor_138, retro_cpor_186 , retro_cpor_365,
Dipodomys ordii	ENSDORG00000014912	1 retrocopy	retro_dord_674,
Monodelphis domestica	ENSMODG00000027710	2 retrocopies	retro_mdom_1275, retro_mdom_776,
Mus musculus	ENSMUSG00000040204	7 retrocopies	retro_mmus_1088, retro_mmus_1289, retro_mmus_1335, retro_mmus_1844, retro_mmus_2809, retro_mmus_2964, retro_mmus_378,
Otolemur garnettii	ENSOGAG00000003982	1 retrocopy	retro_ogar_501,
Rattus norvegicus	ENSRNOG00000016561	5 retrocopies	retro_rnor_1162, retro_rnor_1412, retro_rnor_2595, retro_rnor_2624, retro_rnor_2698,
Ictidomys tridecemlineatus	ENSSTOG00000019643	4 retrocopies	retro_itri_1241, retro_itri_1324, retro_itri_1888, retro_itri_929,
Tupaia belangeri	ENSTBEG00000013732	2 retrocopies	retro_tbel_3099, retro_tbel_4093,