RetrogeneDB ID:

retro_cpor_1130

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_5:1561163..1562234(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF6
Ensembl ID:ENSCPOG00000005116
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1130
TTCAGCACTTTCATCCCAGAGGGAGTCAGGGTCAATGTGGTTTAAAAGAACCTGCTCATGTATCTAATGTGCCTGGTCAA
GGCACTGATGGGCAACCCTACACTGTCTCTAGATAAATACGTGCATGAGCTGATTCCAGTGGTAATGACCTGCATTGTGA
GCAGACAGGTGTGTTTGTGACCTGATATTGACAATCAATGGGCACTCTGGGACTTTGCTGCCTGCCTAGTGGCCCAGATC
TATAAGCATTTCAGCACAACCACTAACAAGTCCCAGTCCCAAATCACAAAGACCTTCACAAAGAGCTTGCTAGACAAGAA
GACTACTTGGACAACTCATTATGGCTCCATTGCCAGCCTAGCAGAGCTGGGATATGATGTGATCAAGACTCTAATTATGC
CCAGGCTGTAGCAGGACAGGGAGCAGATCCACAGTGTCCTGGATGGCCCAGTGCTGAGTAACATGGACCATGTCAGAGCT
CACCATGTGCAGAGCCTCCTTCTGAAACACTGTGCACCTGTACTGGCTATGCTGCATGTCCTGCCTGATAATTAGGATGC
CTATCAGGCAGAATTTGGGTCCCTTGGGCCCCTCCGCTATTCCCATGTAATCAAGGCTCAGGTGCAGGCTGCTCAGCAGG
CACAGCAGGTCAACAGAACCAAACTGATCATCACACAGCCCTGACCCACACAGATCCTATCTCAGGCCCCTCAGTCTGGC
CCTCAGACTTCTGACTTGAAGGTCCTTGGCTCCACCATACTGCCCATCCAGACACTGACATCTGTGCTAGCTGCTGCCCC
ACCTCAGCCTTTCCCTCCTCTAACCAAGTTTTTTGTAAGATCGTCATCCTCTAGGGCCTCCTCCACACAGCAGATCTTGT
CCCTCAGCACCTCTGCCTCTGGCTCAGGATCTACCACTACCTCTCCTGTCACCACCGCAGTCCCCAGCATGTGGCCCATC
GTCAAGCTGGTCTCCACCAACTCCACTGCACCCTCCAGCAAGGTACCCTCTGCTCCTGGCAGTGTCCAGAAGTGCATGGT
AGTCTCACTACCCCCAACAGGAAATGGCAAG

ORF - retro_cpor_1130 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.11 %
Parental protein coverage: 53.1 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFSTFISEGVRVNVVQNNLALLIYLMRMVKALMDNPTLYLEKYVHELIPAVMTCIVSRQLCLRPDVDNHWA
FSTFI.EGVRVNVV..NL..L.YLM..VKALM.NPTL.L.KYVHELIP.VMTCIVSRQ.CL.PD.DN.WA
RetrocopyFSTFIPEGVRVNVV*KNL--LMYLMCLVKALMGNPTLSLDKYVHELIPVVMTCIVSRQVCL*PDIDNQWA
ParentalLRDFAARLVAQICKHFSTTTNNIQSRITKTFTKSWVDEKTPWTTRYGSIAGLAELGHDVIKTLILPRLQQ
L.DFAA.LVAQI.KHFSTTTN..QS.ITKTFTKS..D.KT.WTT.YGSIA.LAELG.DVIKTLI.PRL.Q
RetrocopyLWDFAACLVAQIYKHFSTTTNKSQSQITKTFTKSLLDKKTTWTTHYGSIASLAELGYDVIKTLIMPRL*Q
ParentalEGERIRSVLDGPVLSNIDRIGADHVQSLLLKHCAPVLAKLHPPPDNQDAYRAEFGSLGPLLCSHVVKARA
..E.I.SVLDGPVLSN.D...A.HVQSLLLKHCAPVLA.LH..PDN.DAY.AEFGSLGPL..SHV.KA..
RetrocopyDREQIHSVLDGPVLSNMDHVRAHHVQSLLLKHCAPVLAMLHVLPDN*DAYQAEFGSLGPLRYSHVIKAQV
ParentalQAALQAQQVNRTTLTITQPRPTLTLSQAPQSGPRTPGLLKVPGSIALPVQTLVSARAAAPPQPSPPPTKF
QAA.QAQQVNRT.L.ITQP.PT..LSQAPQSGP.T...LKV.GS..LP.QTL.S..AAAPPQP.PP.TKF
RetrocopyQAAQQAQQVNRTKLIITQP*PTQILSQAPQSGPQTSD-LKVLGSTILPIQTLTSVLAAAPPQPFPPLTKF
ParentalIVMSSSSSASSTQQVLSLSTSAPGSGSTTTSPVTTTVPSVQPIVKLVSTASNAPPSTAPSGPGSVQKYIV
.V.SSSS.ASSTQQ.LSLSTSA.GSGSTTTSPVTT.VPS..PIVKLVST.S.AP.S..PS.PGSVQK..V
RetrocopyFVRSSSSRASSTQQILSLSTSASGSGSTTTSPVTTAVPSMWPIVKLVSTNSTAPSSKVPSAPGSVQKCMV
ParentalVSLPPTGDGK
VSLPPTG.GK
RetrocopyVSLPPTGNGK

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 .00 RPM 53 .49 RPM
SRP017611_kidney 0 .00 RPM 47 .21 RPM
SRP017611_liver 0 .00 RPM 25 .07 RPM
SRP040447_lung 0 .00 RPM 64 .21 RPM
SRP040447_skeletal_muscle 0 .00 RPM 43 .55 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_1130 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1130 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 ENSCPOG00000005116 1 retrocopy
retro_cpor_1130 ,


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