RetrogeneDB ID: retro_cpor_1301

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_67:251227..252067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAK1
• Ensembl ID: ENSCPOG00000000164
• Aliases: None
• Description: None

Sequence

>retro_cpor_1301
GTAGTTACATCTCCTATTTCACCCACTGAGTGTAACACCATTCTGCCAGATGCTTTGACCCAGAATACTAAGAAACAGAA
GAAGCCCAAAATGTCTGATGAGATCTTGGAAAACTTATGGAGCATAGTGAGCGTGGGTGAGCCTAGGAAGAAATATACAC
AATTTGAGAAAGTTGAGCAAGGTTCTTCAGGCACATGTACACTGCCATGGATACAGCCACAGGTTAGGAGGTGACCATTA
AGCAGAGGAGTCTTCAGCAGCAGCCTAAGAAAGAGCTCATTATTAATGAGATCCTAGTCATGAGTGAGAAAGCAAAAATC
CAAATATTGTGAACTACTTGGACAGTTAACTTGTGGGAGATGAGCTGTGGGAATACTTGGCTGGAGGTTCTTTGACAGAT
GTGGTGAAAAAAACTGTATGGATGAAGGCCAGATTGCTGTCATGTGCCATGAGTCTGCAAGCTCTGGAGTTTCTGCACTC
CAACCAAGTCATTCATGGAGACACCGAGAGTGATAATATTCCGTTGGGTATGGATGGCTCTGTCAAGCTAACTGATTTTG
GATTCTGTGCATAAATCACTTCAGAGCAGAGCCAACAGAGCACCATGGTGGGAACTCCATCTTGGATGGCACCAGAGGTT
GTGATGAGGAAGGCGTATGGGCCCAAGGTTGACATCTGGTCCCTAGGCATCATGACCAATAAAATGATTGAAGAGAGCCA
CCATACTCCAATGTAAACCCACTGATAGCCTTGTATCTCATTGTCACCAATGGGATCCCAGAGCTTCCCTGGAGAAGCTA
TCTTCTGAGACTTTTTGAACTGTGGTCTTTAAATGGATGT

Alignment

ORF - retro_cpor_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• Parental protein coverage: 52.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VATSPISPTENNTVLPDALTRNTEKQKKKPKMSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGT-VY
          V.TSPISPTE.NT.LPDALT.NT.KQKK.PKMSDE.ILE.L.SIVSVG.P.KKYT.FEK..QG.SGT..Y
Retrocopy VVTSPISPTECNTILPDALTQNTKKQKK-PKMSDE-ILENLWSIVSVGEPRKKYTQFEKVEQGSSGT<MY

Parental  TAMDVATGQEVAIKQMNLQ-QQPKKELIINEILVMR-ENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLT
          TAMD.ATG.EV.IKQ..LQ.Q..K...I.........E.KNPNIVNYLDS.LVGDELW...EYLAGGSLT
Retrocopy TAMDTATG*EVTIKQRSLQQQPKKELIINEILVMSE<ESKNPNIVNYLDS*LVGDELW---EYLAGGSLT

Parental  DVVTET-CMDEGQIAAV-CRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKR
          DVV..T.CMDEGQI.AV.C...LQALEFLHSNQVIH.D..SDNI.LGMDGSVKLTDFGFCA.IT.EQS..
Retrocopy DVVKKT<CMDEGQI-AV>CAMSLQALEFLHSNQVIHGDTESDNIPLGMDGSVKLTDFGFCA*ITSEQSQQ

Parental  STMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE-GEPPYLNENPLRALYLIATNGTPELQNPEKL
          STMVGTP.WMAPEVV.RKAYGPKVDIWSLGIM...MIE..EPPY.N.NPL.ALYLI.TNG.PEL.....L
Retrocopy STMVGTPSWMAPEVVMRKAYGPKVDIWSLGIMTNKMIE<REPPYSNVNPLIALYLIVTNGIPELPWRSYL

Parental  SAIFRDF-LNRC
          ...F....LN.C
Retrocopy LRLFELWSLNGC

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	114.17 RPM
SRP017611_kidney	0.00 RPM	25.75 RPM
SRP017611_liver	0.00 RPM	2.18 RPM
SRP040447_lung	0.00 RPM	9.96 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1301 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1301 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000164	1 retrocopy	retro_cpor_1301 ,
Pongo abelii	ENSPPYG00000003708	1 retrocopy	retro_pabe_1272,