RetrogeneDB ID:

retro_cpor_279

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_116:3465424..3466137(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KIN
Ensembl ID:ENSCPOG00000010515
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_279
AGGAGATGCTTTGGCACCAAGTGAGTCCATAACAATACAGTTTATGATGAACACAGCAGGAACTGAGAGCACATCCATAG
GAACGCTACTCAGTGGAAAACACTGATGGAATTATACTAAGTGGCTGGGAAGACACGGCCTGTGCCAAAGTGCATGAGGT
CCTCTAAGGCTGGTGTATCCAGCACACTACTGGGGACCCAGAGACTACTCACTGGCAGCTAGGGCGAGGGAAGCAGCATC
AGTATCTTGGCAATAAAGAGTAACCTGCCAAATTTATTGAAGAGCAAGTGCAAAGAGGTCTGAAAAGGAGGAGGAGGAGG
CCCCTGTCTTTATGGAATTCAGCAAAAGAATGATGAAAAAGTCACATTTCACATAAATCAAGGAATACCTAATTTCACCA
GGACCCACATCATACAAATCCTGTTCTTTGGGGCTAAGTGCATGGAAGATGCTTGGGAGAATTGCATCAGTGAAACCAAT
TTCCCAGAGCTCAGCCCAGTCTCAAAAGAAAAAGAAATCCACACTTGTGGAAATCATGGAGATTGAAGAGGAAAAGAACT
CAGATTCTTTGCTACAGCCTGAAATCACTGAAAATTAGAACCAAAAATCTTGCCGAGAAATACCTTCAAAAAACCAGTGT
GCTTAAGGAGGTCATTGACAAATACACAGCCATTATCAAAATGATCGATTCTGGAGACCAGCTGAAGCTTGAA

ORF - retro_cpor_279 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.65 %
Parental protein coverage: 63.1 %
Number of stop codons detected: 4
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalRRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTD-FTKWLGREGLC-KVDETPKGWYIQYIDRDPET
RR.FGTK.VHNN.VY.E.....EHIH.NATQW.TL....TKWLGR.GLC.KV.E...GW.IQ....DPET
RetrocopyRRCFGTK*VHNNTVYDEHSRN*EHIHRNATQWKTLME>YTKWLGRHGLC>KVHEVL*GWCIQHTTGDPET
ParentalIRRQLELEKKKKQDLDDEEKTAKFIEEQVRRGL-EGKEQEAPVFTELSR-ENDEEKVTFNLNKGACS-SS
...QL....K..Q.L...E..AKFIEEQV.RGL.E..E.EAPVF.E.S...ND.EKVTF..N.G....S.
RetrocopyTHWQLG-RGKQHQYLGNKE*PAKFIEEQVQRGL<EKEEEEAPVFMEFSK<KND-EKVTFHINQGIPN>SP
ParentalGATTSKSSSLGPSALKTLGSTASVKRKETSQSSAQSKEKKKKKSALDEIMEIEEEKKRTSRTDYWLQPEI
G.T..KS.SLG.SA.K.LG..ASV..K..SQSSAQS...KKKKS.L.EIMEIEEEK......D..LQPEI
RetrocopyGPTSYKSCSLGLSAWKMLGRIASV--KPISQSSAQS--QKKKKSTLVEIMEIEEEK----NSDSLLQPEI
ParentalIV-KIITKKLGEKYHKK-KGIVKEVIDRYTAVVKMIDSGDKLKLD
...K...K.L.....KK.....KEVID.YTA..KMIDSGD.LKL.
RetrocopyTE<KLEPKILPRNTFKK<TSVLKEVIDKYTAIIKMIDSGDQLKLE

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






(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 .00 RPM 6 .67 RPM
SRP017611_kidney 0 .00 RPM 6 .07 RPM
SRP017611_liver 0 .04 RPM 3 .92 RPM
SRP040447_lung 0 .00 RPM 6 .71 RPM
SRP040447_skeletal_muscle 0 .00 RPM 2 .37 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_279 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_279 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 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000042801 retrocopy
Cavia porcellus ENSCPOG00000010515 5 retrocopies
Dipodomys ordii ENSDORG000000037322 retrocopies
Ficedula albicollis ENSFALG000000018421 retrocopy
Myotis lucifugus ENSMLUG000000022611 retrocopy
Rattus norvegicus ENSRNOG000000266901 retrocopy
Taeniopygia guttata ENSTGUG000000021191 retrocopy



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