RetrogeneDB ID: retro_cpor_1315

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:8897404..8897672(+)
• Located in intron of: ENSCPOG00000006720

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSCPOG00000006301
• Aliases: None
• Description: None

Sequence

>retro_cpor_1315
GATGACAACGCAGAACACCTTCTGGCGCTGACCATGCTCTGCCTTACCAAGGGAGCGAAGAACAAGTGTAACGTAGTGGC
CTGGAACCATGATCACCAGGAGATCTCAGGCCTCGTGGCCAGCCTCAAGTTGTCTTGCCACCCATGCTCAGTTTGGATGA
CTGCTTCCAGCTCCAGCCACCGTAATCTTCCGCCTGAAATGGGGCTCTGGCCGGTTGCGGATCACTGGGCGGCATCATGT
TGTTACTATAAGCAAGGATGTTTCTGAG

Alignment

ORF - retro_cpor_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• Parental protein coverage: 56.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDDAEHVLALTMLCLTEGAKDECNVVEVVARNHDHQEIAVPVANLKLSCQ-PMLSLDD-FQLQPP-VTFR
          .D.AEH.LALTMLCLT.GAK..CNVV...A.NHDHQEI...VA.LKLSC..PMLSLDD.FQLQPP.V.FR
Retrocopy DDNAEHLLALTMLCLTKGAKNKCNVV---AWNHDHQEISGLVASLKLSCH<PMLSLDDCFQLQPP<VIFR

Parental  LKSGSGPVRVTGRHQIVTISNDVAE
          LK.GSG..R.TGRH..VTIS.DV.E
Retrocopy LKWGSGRLRITGRHHVVTISKDVSE

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	2.13 RPM	4.14 RPM
SRP017611_kidney	0.73 RPM	9.74 RPM
SRP017611_liver	0.17 RPM	6.22 RPM
SRP040447_lung	0.63 RPM	10.49 RPM
SRP040447_skeletal_muscle	0.16 RPM	9.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1315 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1315 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315 ,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,