RetrogeneDB - Retrocopy retro_cjac

                        
>retro_cjac_766
GTGGAAGCAGATATAATTGCAAATCTTTCATGCAAGCTCAAAGAAGTTGAAGAAGAGAGACTAAAAGCTGCGCAGTACGG

TTTACAACTAGTAGAGAGTCAAAATGAATTATAGAATCAATTGGATAAATGTCGTAATGAAATGATGACCATGACTGAGA

GTTATGAACATGAAAAATATACCCTTCAAAGAGAAGTTGAACTCAAGAGTCGAATGTTAGAAAGTTTGAGCTCTGAATGT

GAAGTTATTAAACAACAAAAAATACACCTGGAGTAATTGGAAGAACAACTAAACAGAAGCCATGGGCAGGAAGTGAATGA

ACTAAAAACTAAGATAGAAAAATTGAAAGTGGAATTAGATGAAGCTAGGCTTAGTGAAAAACAGTTGAAGCACCAAATGG

ATCATCAGAAGGAACTCCTCTCTTGTAACTCAGAGGAACTGTGCATAATGTCTGGACGTGTGCAGGAAAGCATGTCTTCA

GAGATGCTGGCTCTTCAAATTGAGCTGACAGAAATGGAGAGTATGATGACCACCCTCAAAGAAGTGAATGAACTACAAAA

CAGACAAGAACAGCTAGAACTTATTACTAACCTAATGCATCAGGTAGACCAGCCTTTTAAAGAGGAAAAAGAGGAGCAAG

AAAAAGAAGCAGATTCTTACTATAATGCTCTAGAGAAAGCTCATGTAGCAAATGAAGATCTTCAGGTGCAGTTGGACCAG

GCAATCCAGCAAGCCTTGGATCCTAATAGTAAAGGCAACTCTTTGTTTGCAGAGGTAGAAGATCGAAGGGCAGCAATGGA

ATGTCAGCTTATCAGTATGAAAGTCAAGTATCAGTCACTAAGGAAGCAAAATGTATTTAACAGAGAGCAGATGCAGAGAA

TGAAGTTACAAATCGCCACATTGCTACAGATCAAAGGGTCTCAAACTGAATTTGAGCAGCAGGAACGGTTGCTTGCCATG

TTGGAGCAGAAGAATGGTGAAATAAAACATCTTTTAGGTGAAATTAGAAATCTGGAGAAAGTTAAGAATTTATATGAAAG

TATGGAATCTAAGCCTTCACTCCACTCTGGTACTCTG

ORF - retro_cjac_766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	90.06 %
Parental protein coverage:	59.67 %
Number of stop codons detected:	2
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMEADIIANLRCKLKEAEEERLKAAQYGLQLVESQNELQNQLDKCRNEMMTMTESYEQEKYTLQREVELKS
.EADIIANL.CKLKE.EEERLKAAQYGLQLVESQNEL.NQLDKCRNEMMTMTESYE.EKYTLQREVELKS
RetrocopyVEADIIANLSCKLKEVEEERLKAAQYGLQLVESQNEL*NQLDKCRNEMMTMTESYEHEKYTLQREVELKS
ParentalRMLESFSSECEVIKQQQKIHLEKLEQQLSRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQIDHQKEL
RMLES.SSECEVIKQQ.KIHLE.LE.QL.RSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQ.DHQKEL
RetrocopyRMLESLSSECEVIKQQ-KIHLE*LEEQLNRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQMDHQKEL
ParentalLSCKSEELRIMSGRVQESMSSEMLALQIELTEMESMKTTLTEEVNELQYRQEQLELLITNLMRQVDR-LK
LSC.SEEL.IMSGRVQESMSSEMLALQIELTEMESM.TTL..EVNELQ.RQEQLEL.ITNLM.QVD...K
RetrocopyLSCNSEELCIMSGRVQESMSSEMLALQIELTEMESMMTTL-KEVNELQNRQEQLEL-ITNLMHQVDQPFK
ParentalEEKDEREKEAVSYYNALEKARVANQDLQVQLDQALQQALDSNSKGNSLFAEVEDRRAAMERQLITMKVKY
EEK.E.EKEA.SYYNALEKA.VAN.DLQVQLDQA.QQALD.NSKGNSLFAEVEDRRAAME.QLI.MKVKY
RetrocopyEEKEEQEKEADSYYNALEKAHVANEDLQVQLDQAIQQALDPNSKGNSLFAEVEDRRAAMECQLISMKVKY
ParentalQSLKKQNVFNREQMQRMKLQIATLLQMKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKFKNLYES
QSL.KQNVFNREQMQRMKLQIATLLQ.KGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEK.KNLYES
RetrocopyQSLRKQNVFNREQMQRMKLQIATLLQIKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKVKNLYES
ParentalMESKPSVHSGAL
MESKPS.HSG.L
RetrocopyMESKPSLHSGTL

                            

                            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
SRP051959_colon	0 .27 RPM	4 .50 RPM
SRP051959_heart	0 .14 RPM	3 .42 RPM
SRP051959_kidney	0 .16 RPM	2 .11 RPM
SRP051959_liver	0 .09 RPM	1 .30 RPM
SRP051959_lung	0 .31 RPM	3 .56 RPM
SRP051959_lymph_node	0 .46 RPM	3 .88 RPM
SRP051959_skeletal_muscle	0 .13 RPM	2 .29 RPM
SRP051959_spleen	0 .27 RPM	4 .79 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_766 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_766 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_766 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013141	5 retrocopies	retro_chof_1356, retro_chof_1565, retro_chof_1882, retro_chof_198, retro_chof_2505,
Callithrix jacchus	ENSCJAG00000004745	1 retrocopy	retro_cjac_766 ,

	RetrogeneDB ID:	retro_cjac_766
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	10:20906114..20907191(-)
	Located in intron of:	ENSCJAG00000002506
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SPDL1
	Ensembl ID:	ENSCJAG00000004745
	Aliases:	None
	Description:	spindle apparatus coiled-coil protein 1 [Source:HGNC Symbol;Acc:26010]

Parental	MEADIIANLRCKLKEAEEERLKAAQYGLQLVESQNELQNQLDKCRNEMMTMTESYEQEKYTLQREVELKS
	.EADIIANL.CKLKE.EEERLKAAQYGLQLVESQNEL.NQLDKCRNEMMTMTESYE.EKYTLQREVELKS
Retrocopy	VEADIIANLSCKLKEVEEERLKAAQYGLQLVESQNEL*NQLDKCRNEMMTMTESYEHEKYTLQREVELKS

Parental	RMLESFSSECEVIKQQQKIHLEKLEQQLSRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQIDHQKEL
	RMLES.SSECEVIKQQ.KIHLE.LE.QL.RSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQ.DHQKEL
Retrocopy	RMLESLSSECEVIKQQ-KIHLE*LEEQLNRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQMDHQKEL

Parental	LSCKSEELRIMSGRVQESMSSEMLALQIELTEMESMKTTLTEEVNELQYRQEQLELLITNLMRQVDR-LK
	LSC.SEEL.IMSGRVQESMSSEMLALQIELTEMESM.TTL..EVNELQ.RQEQLEL.ITNLM.QVD...K
Retrocopy	LSCNSEELCIMSGRVQESMSSEMLALQIELTEMESMMTTL-KEVNELQNRQEQLEL-ITNLMHQVDQPFK

Parental	EEKDEREKEAVSYYNALEKARVANQDLQVQLDQALQQALDSNSKGNSLFAEVEDRRAAMERQLITMKVKY
	EEK.E.EKEA.SYYNALEKA.VAN.DLQVQLDQA.QQALD.NSKGNSLFAEVEDRRAAME.QLI.MKVKY
Retrocopy	EEKEEQEKEADSYYNALEKAHVANEDLQVQLDQAIQQALDPNSKGNSLFAEVEDRRAAMECQLISMKVKY

Parental	QSLKKQNVFNREQMQRMKLQIATLLQMKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKFKNLYES
	QSL.KQNVFNREQMQRMKLQIATLLQ.KGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEK.KNLYES
Retrocopy	QSLRKQNVFNREQMQRMKLQIATLLQIKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKVKNLYES

Parental	MESKPSVHSGAL
	MESKPS.HSG.L
Retrocopy	MESKPSLHSGTL

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

RetrogeneDB ID:

retro_cjac_766