RetrogeneDB ID: retro_cpor_1497

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:28591509..28591941(-)
• Located in intron of: ENSCPOG00000013843

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16ORF96
• Ensembl ID: ENSCPOG00000023268
• Aliases: None
• Description: None

Sequence

>retro_cpor_1497
CCACAGCTGATCACCATTCGTAAGAGTCTATCTACTGTTGAGGCTGGGGGCAGCCATTGCCAAACAGCTATGAGTACCTG
TAGTGTCAGCAGATGAGGGCATGTTAGCAGCTGCTGTTACAGGAGCTTGGCATCCCAGAGGAAAGCCTGTATGCCCTGGT
TCCCACCAGGATTGGCATGACAGCCTTGAAATGATGCCAGCATCAAGCTCCAGTCTTGTAATCTTTCAACTCTTTCCATT
TATGGGGATCCTCAGGTGATAGACTATGACACTACTAAGGTGGACAAGCTAGGGTGGATGGGCTGCAGTACAAAGATTGG
AACAACCAGATTGGGACTCAACCCTTGGCCGTTGAGGAAAGAGCTAGTTTTGAAGATTCCATGTCCCCAGGCTCAAAATA
CGTATGACCATGTGCCCTATAGTTCCTTAATT

Alignment

ORF - retro_cpor_1497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.25 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PQLITIR-RAHLLSRLRPASA-NSYEYLQRQQMREQHQLHFQHLSTTEDSFDPL-SSHQDWNDG-PRNDP
          PQLITIR.R..LL.RL..A.A.NSYEYL..QQMR...QL..Q.L...E.S...L..SHQDW.D..P.ND.
Retrocopy PQLITIR>RVYLLLRLGAAIA>NSYEYL*CQQMRAC*QLLLQELGIPEESLYAL<GSHQDWHDS<P*NDA

Parental  NLKLKSYNLSTLYPYGDPQVIDYDTAEVDILG-VDGILYKGRMTNQTGTRLLATGEKEPAVMKIPCPPG-
          ..KL.S.NLSTL..YGDPQVIDYDT..VD.LG.VDG..YK....NQ.GT..LA..E...A.......PG.
Retrocopy SIKLQSCNLSTLSIYGDPQVIDYDTTKVDKLG<VDGLQYKD-WNNQIGTQPLAVEER--ASFEDSMSPG>

Parental  QSLCDRVRSSALV
          Q...D.V..S.L.
Retrocopy QNTYDHVPYSSLI

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	1.15 RPM
SRP017611_kidney	0.42 RPM	0.10 RPM
SRP017611_liver	0.13 RPM	0.09 RPM
SRP040447_lung	0.03 RPM	1.01 RPM
SRP040447_skeletal_muscle	0.03 RPM	0.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1497 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1497 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023268	1 retrocopy	retro_cpor_1497 ,