RetrogeneDB ID: retro_cpor_1298

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_67:4277929..4278168(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM18
• Ensembl ID: ENSCPOG00000012522
• Aliases: None
• Description: None

Sequence

>retro_cpor_1298
AGCACCTTCCCTGCCAGCATCCCAGCAGTGATCAGGACAGACTGGACTGAGCCGTGGCTCTTGGGGCCGGCTGTGTTCCA
CATCCTGTTCCTGCTCCTCACTACTTCTCCTCCCAGAGACACAGACTACAGACCGTTCTCTTCTTGTGCCTCATTGCTTC
AGTCTACTGCATTGAGCACATCAACGAAGTGGCTGCCGTGAACTTGAGGTTGTTTCCCAAATACCAGTATTTTGACTCA

Alignment

ORF - retro_cpor_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 57.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SYFPVSIPSVIMQTDWTEPWLLGLVAFHVLCLLLTC-FSAQRYQLQVGLFLSLAALVYCAEYINEVAAMN
          S.FP.SIP.VI..TDWTEPWLLG...FH.L.LLLT..FS.QR..LQ..LFL.L.A.VYC.E.INEVAA.N
Retrocopy STFPASIPAVI-RTDWTEPWLLGPAVFHILFLLLTT<FSSQRHRLQTVLFLCLIASVYCIEHINEVAAVN

Parental  WRSFSKYQYFDS
          .R.F.KYQYFDS
Retrocopy LRLFPKYQYFDS

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	3.51 RPM
SRP017611_kidney	0.00 RPM	13.40 RPM
SRP017611_liver	0.00 RPM	6.66 RPM
SRP040447_lung	0.00 RPM	14.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.29 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1298 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1298 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000543	1 retrocopy	retro_chof_31,
Cavia porcellus	ENSCPOG00000012522	1 retrocopy	retro_cpor_1298 ,
Dipodomys ordii	ENSDORG00000001854	1 retrocopy	retro_dord_416,
Equus caballus	ENSECAG00000008640	1 retrocopy	retro_ecab_596,
Monodelphis domestica	ENSMODG00000014284	1 retrocopy	retro_mdom_790,