RetrogeneDB ID: retro_cpor_1121

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_48:2214127..2214482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGS2
• Ensembl ID: ENSCPOG00000011598
• Aliases: None
• Description: None

Sequence

>retro_cpor_1121
ATTCAAAGTGCTATGCTCTTGGCTGTCCGGCACGATTGTGTACCAATAGACAAGAGTGCAATCAGCAGACCCAAAAGTGA
GAAGAGGTGGGAAAAGATGAAATGGATGCTCCTAAAAGATTGGAAAATCCATCTGAACTACTTTTTGCAAAATTCTTCTA
CACCTGCGAAGCCCAAAGTCAGCAAGAAAAACAAACAGCAAACTTTCATCATACCTTCTCCTGGGAAAGCACTGCTATGG
TCAGAAGCCTTTCATGAATTGCTAGCTAGTAAATATGGTCTTGTTGCATTTAGGGCTTTTTTAAAAATCTGAGCTCTGTG
AAGAAAATATTGAATTCTGGTTAGCTTGTGAAGAC

Alignment

ORF - retro_cpor_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSAMFLAVQHDCVPMDKSAGSGSKSEEKREKMKRTLLKDWKTRLSYFLQNSSTPAKPKTSKKSKQQTFI
          .QSAM.LAV.HDCVP.DKSA.S..KSE...EKMK..LLKDWK..L.YFLQNSSTPAKPK.SKK.KQQTFI
Retrocopy IQSAMLLAVRHDCVPIDKSAISRPKSEKRWEKMKWMLLKDWKIHLNYFLQNSSTPAKPKVSKKNKQQTFI

Parental  KPSPEEALLWSEAFDELLASKYGLAAFRAFL-KSEFCEENIEFWLACED
          .PSP..ALLWSEAF.ELLASKYGL.AFRAFL.KSE.CEENIEFWLACED
Retrocopy IPSPGKALLWSEAFHELLASKYGLVAFRAFL>KSELCEENIEFWLACED

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	5.41 RPM
SRP017611_kidney	0.00 RPM	1.99 RPM
SRP017611_liver	0.00 RPM	3.00 RPM
SRP040447_lung	0.00 RPM	14.68 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.10 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1121 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1121 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034366	1 retrocopy	retro_btau_1349,
Cavia porcellus	ENSCPOG00000011598	1 retrocopy	retro_cpor_1121 ,
Macropus eugenii	ENSMEUG00000007191	1 retrocopy	retro_meug_1498,
Monodelphis domestica	ENSMODG00000012101	1 retrocopy	retro_mdom_690,