RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_16
CGCAAGCAGCAGTCTCTGGTCCCAGCCCACCCCATGGCCCCTCCCAGTCCCAGCACCACCAGCAGTAATAACAACAGTAG

CAGCAGCAGCAACTCAGGATGGGATCAGCTCAGCAAAACGAACCTCTATATCCGAGGACTGCCTCCCCACACCACCGACC

AGGACCTGGTGAAGCTCTGTCAACCATATGGGAAAATAGTCTCCACAAAGGCAATTTTGCATAAGACAACGAACAAATGC

AAAGGTTATGGTTTTGTCGACTTTGACAGCCCTGCAGCAGCTCAAAAAGCTGTGTCTGCCCTGAAGGCCAGTGGGGTTCA

AGCTCAAATGGCAAAGCAACAGGAACAAGATCCTACCAACCTCTACATTTCTAATTTGCCACTCTCCATGGATGAGCAAG

AACTAGAAAATATGCTCAAACCATTTGGACAAGTTATTTCTACAAGGATACTACGTGATGCCACTGGTACAAGTCGTGGT

GTTGGCTTTGCTAGGACGGAATCAACAGAAAAATGTGAAGCTGTTACTGGTCATTTTAATGGAAAATTTATTAAGGCACC

ACCAGGAGTTTCTGCCCCCACAGAACCTTTATTGTGTAAGTTTTCTGATGGAGGACAGAAAAAGAGACAGAACCCAAACA

AATACATCCCTAATGGAAGACCATGGCATAGAGAAGGAGAGGTGAGACTTACTGGAATGACACTTACTTACGACCCAACT

ACAGCTGCTATACAGAACGGATTTTATCCTTCACCATACAGTATTGCTACAAACCGAATGATCACTCAAACTTCTATTAC

ACCCTATATTGCATCTCCTGTATCTGCCTACCAGGTGCAAAGTCCTTCTTGGACGCAACCTCAACCATATATTCTACAGC

ACCCCGGTGCCGTGTTAACTCCCTCAATGGAGCACACCATGTCACTACAGCCCGCATCAATGATCAGCCCTCTGGCCCAG

CAGATGAGTCATCTGTCACTAGGCAGCACCGGAACATACATGCCTGCAACGTCAGCTATGCAAGGAGCCTACTTGCCACA

GTATGAACATATGCAGACGACAGCGGCTCCTGTTGAGGAGGCAAGTGGTCAACAGCAGGTGGCTGTCGCGACGTCTAATG

ACCATTCTCCATATACCTTTCAACCTAATAAG

ORF - retro_ptro_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.61 %
Parental protein coverage:	74.6 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalKQSYAPAPHPMAPPSPSTNSSSNNSSN--NSSGEQLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKA
.QS..PA.HPMAPPSPST.SS.NNSS...NS...QLSKTNLYIRGLPP.TTDQDL.KLCQPYGKIVSTKA
RetrocopyQQSLVPA-HPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVSTKA
ParentalILDKNTNQCKGYGFVDFDSPAAAQKAVASLKANGVQAQMAKQQEQDPTNLYISNLPISMDEQELENMLKP
IL.K.TN.CKGYGFVDFDSPAAAQKAV..LKA.GVQAQMAKQQEQDPTNLYISNLP.SMDEQELENMLKP
RetrocopyILHKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKP
ParentalFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFNGKYLKTPPGIPAPSEPLLCKFADGGQKKRQN
FG.VISTRILRDA.G.SRGVGFAR.ESTEKCE.V..HFNGK..K.PPG..AP.EPLLCKF.DGGQKKRQN
RetrocopyFGQVISTRILRDATGTSRGVGFARTESTEKCEAVTGHFNGKFIKAPPGVSAPTEPLLCKFSDGGQKKRQN
ParentalQSKYTQNGRPWPREGE---AGMALTYDP-TAAIQNGFYSSPYSIATNRMIPQTSITPFIAASPVSTYQVQ
..KY..NGRPW.REGE....GM.LTYDP.TAAIQNGFY.SPYSIATNRMI.QTSITP.I.ASPVS.YQVQ
RetrocopyPNKYIPNGRPWHREGEVRLTGMTLTYDPTTAAIQNGFYPSPYSIATNRMITQTSITPYI-ASPVSAYQVQ
ParentalSTSWMPHPPYVMQPTGAVITPTMDHPMSMQPANMMGPLTQQMNHLSLGTTGT
S.SW....PY..Q..GAV.TP.M.H.MS.QPA.M..PL.QQM.HLSLG.TGT
RetrocopySPSWTQPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGT

                            

                            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
SRP007412_brain_prefrontal_cortex	1 .30 RPM	1 .77 RPM
SRP007412_cerebellum	0 .57 RPM	0 .93 RPM
SRP007412_heart	1 .22 RPM	5 .51 RPM
SRP007412_kidney	2 .85 RPM	3 .74 RPM
SRP007412_liver	0 .95 RPM	1 .93 RPM
SRP007412_testis	1 .90 RPM	2 .32 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_16 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_16 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_16 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1131

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pan troglodytes	ENSPTRG00000014709	1 retrocopy	retro_ptro_16 ,

	RetrogeneDB ID:	retro_ptro_16
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	12:22995956..22997108(+)
	Located in intron of:	ENSPTRG00000005187
Retrocopy information	Ensembl ID:	ENSPTRG00000039358
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	RBMS3
	Ensembl ID:	ENSPTRG00000014709
	Aliases:	None
	Description:	None

Parental	KQSYAPAPHPMAPPSPSTNSSSNNSSN--NSSGEQLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKA
	.QS..PA.HPMAPPSPST.SS.NNSS...NS...QLSKTNLYIRGLPP.TTDQDL.KLCQPYGKIVSTKA
Retrocopy	QQSLVPA-HPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVSTKA

Parental	ILDKNTNQCKGYGFVDFDSPAAAQKAVASLKANGVQAQMAKQQEQDPTNLYISNLPISMDEQELENMLKP
	IL.K.TN.CKGYGFVDFDSPAAAQKAV..LKA.GVQAQMAKQQEQDPTNLYISNLP.SMDEQELENMLKP
Retrocopy	ILHKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKP

Parental	FGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFNGKYLKTPPGIPAPSEPLLCKFADGGQKKRQN
	FG.VISTRILRDA.G.SRGVGFAR.ESTEKCE.V..HFNGK..K.PPG..AP.EPLLCKF.DGGQKKRQN
Retrocopy	FGQVISTRILRDATGTSRGVGFARTESTEKCEAVTGHFNGKFIKAPPGVSAPTEPLLCKFSDGGQKKRQN

Parental	QSKYTQNGRPWPREGE---AGMALTYDP-TAAIQNGFYSSPYSIATNRMIPQTSITPFIAASPVSTYQVQ
	..KY..NGRPW.REGE....GM.LTYDP.TAAIQNGFY.SPYSIATNRMI.QTSITP.I.ASPVS.YQVQ
Retrocopy	PNKYIPNGRPWHREGEVRLTGMTLTYDPTTAAIQNGFYPSPYSIATNRMITQTSITPYI-ASPVSAYQVQ

Parental	STSWMPHPPYVMQPTGAVITPTMDHPMSMQPANMMGPLTQQMNHLSLGTTGT
	S.SW....PY..Q..GAV.TP.M.H.MS.QPA.M..PL.QQM.HLSLG.TGT
Retrocopy	SPSWTQPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGT

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

RetrogeneDB ID:

retro_ptro_16