RetrogeneDB ID:

retro_cpor_569

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_2:12876249..12877285(+)
Located in intron of:ENSCPOG00000007869
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB11FIP2
Ensembl ID:ENSCPOG00000000453
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_569
ATAATACTGTCAGAGCAAGCCCTAAAGTCATTCCTACTCTATTGCACAGGTCACAGTGCTTCACGGCAAAGATCTGAAGC
CAGAAGGCAAAAGTGGCACCAGTGTATATACACTATAATTCATTTGGGCAAGAAAAAGTATCCTACCTTGTAGCTGACAA
AACCCTTAAGCCAATTTGGAAGGAAGAGGCCTCCTCTGAGCCACTAGATTGCTAATGGAGGGAAATCCAGAGAAATAATT
CTTGTCTTTAGTTATACACAGATCACTAGTAGGTCTGGATAAATTTCTAGGGCAGGTGGCAGTTAAGCTCAGTGACACCT
TTGAGGACAAACAAAGAAGGAAAACAGTAGTTTGGATTAGAATCCAAACAAGGAAAAAGAGTCAAAAACAGGGATGCAAT
AAAGGTCAATATTCAGTTTATGAGGAAAAAGATGACAGCAACTATGTTTGACTTATCAAAGAAGGACAAAACAAGGTCTG
CAAAATTAAAAGATAAGATGAAAGGTAGAAAAAATGGTGGGGTATTTTCTGATATGTCTTCTGCATTCATTCCAAGTACT
CACATGCCTGATGCCAGCGTTGAGTTTCAAGTGGTGAAGTACAAATGAAATCCAAACTGAAAAAGCCTTTTCTTTTGGGT
CCTCAGAATTTCTCTTTTGCACATTCATTGTCTGATTTAACTGAGTCCCACGCATCTTCTGAGAAACTAACGTGTGGTGC
TGTAGGTGAAACACATCTTCTTGGATGCCAGATAGATTCCTTTGGAGCAGTTTCCAGAGAGTAGAAGTCTCAAATCTCCA
CACAGAAGGATTTTGAGCTTTTGCACTTTTAAAATGAACCAACCTGACAGCATTGTGGATGAAGGTAAATTGTCTTTTGG
AAGACAAAATGACCTATTTGCAAACATGACTGCTTCATTACCCCCAAATTTGCAACATTGCCAAGAAAGGAAAATTTATT
TGAAGAAAACTGTGAGTCATGAGACAATAATATGAATTTGTTTTCAAAATCAATTGAAGTAAGAAAAGGGAGCAAG

ORF - retro_cpor_569 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.46 %
Parental protein coverage: 68.36 %
Number of stop codons detected: 3
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalMMLSEQAQKWFPTH-VQVTVLQAKDLKPKGKSGTND-TYTIIQLGKEKYSTS-VAEKTLEPVWKEEASFE
..LSEQA.K.F.....QVTVL..KDLKP.GKSGT....YTII.LGK.KY.T..VA.KTL.P.WKEEAS.E
RetrocopyIILSEQALKSFLLY>AQVTVLHGKDLKPEGKSGTSV<IYTIIHLGKKKYPTL<VADKTLKPIWKEEASSE
Parental-LPGLLMQGNPEKYILFLIVMHRSLVGLDKFLGQVAINLNDIFEDKQRRRT-EWFRLESKQGKSIKNRGE
....LLM.GNPEK..L.L...HRSLVGLDKFLGQVA..L.D.FEDK..RR....F.LESKQGK..KNR..
Retrocopy<ATRLLMEGNPEK*FLSLVI-HRSLVGLDKFLGQVAVKLSDTFEDK-QRRK>Q*FGLESKQGKRVKNRDA
ParentalIKVNIQFMRNNMTASMFDLSMKDKTRSPFAKLKDKMKGRKNDGTFSDTSSAIIPSTHMPDANTEF-SSGE
IKVNIQFMR..MTA.MFDLS.KDKTRS..AKLKDKMKGRKN.G.FSD.SSA.IPSTHMPDA..EF.SSGE
RetrocopyIKVNIQFMRKKMTATMFDLSKKDKTRS--AKLKDKMKGRKNGGVFSDMSSAFIPSTHMPDASVEF<SSGE
ParentalILMKSKPKKPFLLGPQRLSSAHSMSDLTGSHASSEKLKSGAVGQTHLLGCRIDSFGAV-PESGSLKSPHR
..MKSK.KKPFLLGPQ..S.AHS.SDLT.SHASSEKL..GAVG.THLLGC.IDSFGAV.PES.SLKSPHR
RetrocopyVQMKSKLKKPFLLGPQNFSFAHSLSDLTESHASSEKLTCGAVGETHLLGCQIDSFGAV>PESRSLKSPHR
ParentalRTLSFDTSKMNQPDSIVDEGELSFGRQNDLFTNVTASLP-QKFATLPRKKNPFEESSESWDSSMNLFSKS
R.LSF.T.KMNQPDSIVDEG.LSFGRQNDLF.N.TASLP..KFATLPRK.N.FEE..ES.D..MNLFSKS
RetrocopyRILSFCTFKMNQPDSIVDEGKLSFGRQNDLFANMTASLP<PKFATLPRKENLFEENCES*DNNMNLFSKS
ParentalIEVRKENK
IEVRK..K
RetrocopyIEVRKGSK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .29 RPM 24 .67 RPM
SRP017611_kidney 0 .10 RPM 11 .10 RPM
SRP017611_liver 0 .00 RPM 4 .18 RPM
SRP040447_lung 0 .13 RPM 7 .36 RPM
SRP040447_skeletal_muscle 0 .01 RPM 6 .56 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_569 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_569 was not experimentally validated.

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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000000453 1 retrocopy
retro_cpor_569 ,




Copyright © RetrogeneDB 2014-2017