RetrogeneDB ID: retro_cpor_1277

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_63:3251073..3251418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSCPOG00000014413
• Aliases: None
• Description: None

Sequence

>retro_cpor_1277
GGAGTAAAAGTCTCCTGCAATTTCCAGCTGTTGGAAGAACTCAAAGGCCAGAAAGGAGAAGGATAGAGTGCAGTTAATGG
GGGTCTAGAAGATGACGAAGACATGAAACTTACAAGATGGACAGGGATGGCATTTGGGCCTCCAAGAACAATTTATGAAA
ACCGAATATACCTTAAAATAGAATGCGGACCTAAATACCCAGAAGCACCTCCTTGAAAAGACTTGAAACAAAATTTAATA
TGAATGAGTTAATAGCTCCAATGGAGTGGTGAACCCCAGAGCCGTATCAGTGCTAGCAGAAGGCAGAATTCAGATAGCAT
CAGAGATGTTCTGCAAGAGCTTCGG

Alignment

ORF - retro_cpor_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.94 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPE
          GVKV..NF.LLEEL..GQKG.G...V..GLEDDEDM.LTRWTGM..GPPRT.YENRIY.LK.ECGPKYPE
Retrocopy GVKVSCNFQLLEELK-GQKGEG*SAVNGGLEDDEDMKLTRWTGMAFGPPRTIYENRIY-LKIECGPKYPE

Parental  APP-SVRFVTKINMNG-INNSSGMVDARSIPVLA-KWQNSYSIKVVLQELR
          APP...R..TK.NMN...N.S.G.V..R...VLA...QNS.SI..VLQELR
Retrocopy APP<LKRLETKFNMNE<VNSSNGVVNPRAVSVLA<RRQNSDSIRDVLQELR

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	19.10 RPM
SRP017611_kidney	0.00 RPM	11.20 RPM
SRP017611_liver	0.00 RPM	9.14 RPM
SRP040447_lung	0.00 RPM	12.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1277 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1277 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 10 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028827	1 retrocopy	retro_cfam_1223,
Cavia porcellus	ENSCPOG00000014413	4 retrocopies	retro_cpor_1277 , retro_cpor_540, retro_cpor_751, retro_cpor_849,
Felis catus	ENSFCAG00000007602	6 retrocopies	retro_fcat_1169, retro_fcat_1256, retro_fcat_141, retro_fcat_15, retro_fcat_1678, retro_fcat_1868,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Myotis lucifugus	ENSMLUG00000002057	6 retrocopies	retro_mluc_1077, retro_mluc_2371, retro_mluc_386, retro_mluc_559, retro_mluc_659, retro_mluc_985,
Macaca mulatta	ENSMMUG00000008223	1 retrocopy	retro_mmul_1066,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mustela putorius furo	ENSMPUG00000001010	2 retrocopies	retro_mputfur_460, retro_mputfur_979,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Tupaia belangeri	ENSTBEG00000015720	27 retrocopies	retro_tbel_1333, retro_tbel_1456, retro_tbel_1479, retro_tbel_1551, retro_tbel_160, retro_tbel_1740, retro_tbel_1784, retro_tbel_2129, retro_tbel_2149, retro_tbel_2317, retro_tbel_2334, retro_tbel_2496, retro_tbel_2890, retro_tbel_2935, retro_tbel_3021, retro_tbel_3102, retro_tbel_3141, retro_tbel_3461, retro_tbel_3573, retro_tbel_3734, retro_tbel_3935, retro_tbel_3971, retro_tbel_4227, retro_tbel_4319, retro_tbel_4720, retro_tbel_640, retro_tbel_909,