RetrogeneDB ID: retro_cpor_377

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_138:1000029..1000829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKT3
• Ensembl ID: ENSCPOG00000015504
• Aliases: None
• Description: None

Sequence

>retro_cpor_377
ATAGAAATGGATGAAGTGGCACACACTCTAACTGAAAGCAGAGTATTAAAGAACAATAGACATCCATTTTTAACATCATT
GAAATACTACTTCCACACAAAAGACTGTTTGTGTTTTGTGATGGAATATGTTAATGACGGAGAGCTGTTTTTCTATTTGT
CAAGAGAGTGGGTGTTCTCTGAGAACTGCACATGTTTCTATGTTGCAGAAATTGTCTCAGCCTTGGACTATCTACATTCC
AGAAAGATTGTGTACCATGATCTCAAGTTGGAGAATTTGATGCTGGATAAAGATGGCCACATAACAATTACAGATTTTGG
ACTTTGCAAAGAAGGGATCACAGGTGTAGCCACCATGAAGACATTCTGAGGCACACCAGAATACCTGGCACCAGAGGTGT
TAGAAGACAATGACTACAGCCACTCTGTCGACTGGTGGGGCCTGGGGGTTGTCATGTATGAGATGGTGTGTGGAAGGTTA
CCTTTCTACAACCAAGACCATGAGAAATTTTTGAACTAATACTAATAGAAGACATTAAATTTCCACAAACACTCTCTTCA
GATGCAAAATCATTGCTTTCAGGGCTCTTGATAAAGGATCAAAATAAACAACCTGATGGAGGACAAGATGATGCAAAAGA
AATTATGAAACACAGTTTCTTCTCTGGAGTAAACTGGCAAGATGTATATGATAAAAAGCTTGCACCTCCTTTTAAGCCTC
AAGTAACATCTGAGACACACACCAGATATTTTAATAAAGAATTCACAGCTGAGACTATTACAATAACACCACTTGAAAAA

Alignment

ORF - retro_cpor_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 55.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAKDEVAHTLTESRVLKNTRHPFLTSLKYSFQTKDRLCFVMEYVNGGEAVFHLSRERV-SEDRTRFYGAE
          I..DEVAHTLTESRVLKN.RHPFLTSLKY.F.TKD.LCFVMEYVN.GE..F.LSRE.V.SE..T.FY.AE
Retrocopy IEMDEVAHTLTESRVLKNNRHPFLTSLKYYFHTKDCLCFVMEYVNDGELFFYLSREWVFSENCTCFYVAE

Parental  IVSALDYLHSGKIVYRDLKLENLMLDKDGHIKITDFGLCKEGITDAATMKTFCGTPEYLAPEVLEDNDYG
          IVSALDYLHS.KIVY.DLKLENLMLDKDGHI.ITDFGLCKEGIT..ATMKTF.GTPEYLAPEVLEDNDY.
Retrocopy IVSALDYLHSRKIVYHDLKLENLMLDKDGHITITDFGLCKEGITGVATMKTF*GTPEYLAPEVLEDNDYS

Parental  RAVDWWGLGVVMYEMMCGRLPFYNQDHEK-LFELILMEDIKFPRTLSSDAKSLLSGLLIKDPNKRLGGGP
          ..VDWWGLGVVMYEM.CGRLPFYNQDHEK..FELIL.EDIKFP.TLSSDAKSLLSGLLIKD.NK...GG.
Retrocopy HSVDWWGLGVVMYEMVCGRLPFYNQDHEK<IFELILIEDIKFPQTLSSDAKSLLSGLLIKDQNKQPDGGQ

Parental  DDAKEIMRHSFFSGVNWQDVYDKKLVPPFKPQVTSETDTRYFDEEFTAQTITITPPEK
          DDAKEIM.HSFFSGVNWQDVYDKKL.PPFKPQVTSET.TRYF..EFTA.TITITP.EK
Retrocopy DDAKEIMKHSFFSGVNWQDVYDKKLAPPFKPQVTSETHTRYFNKEFTAETITITPLEK

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	0.23 RPM	100.31 RPM
SRP017611_kidney	0.00 RPM	9.11 RPM
SRP017611_liver	0.04 RPM	3.35 RPM
SRP040447_lung	0.13 RPM	26.15 RPM
SRP040447_skeletal_muscle	0.04 RPM	4.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_377 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_377 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	ENSCPOG00000015504	1 retrocopy	retro_cpor_377 ,