RetrogeneDB - Retrocopy retro_vpac

                        
>retro_vpac_197
CAGGTGAATGTGCCAAAAATGCCTACAAATCAGAATGTTTCTCCATCCCGGAGAGATGAAGTGATTCAGTGGCTGGCCAA

ACTCAAGTACCAATTCAGTCTTTACCCAGAAACATATGCACTGGCTAGTAGTCTTTTGCACAGATTCTTAGCTACTGTGA

AGGCCCACCCAAAGCACTTGAGTTGTAGTGCAATCGAATGTTTTTTCCTGGCTGCCAAGACTGTTGAGGAGGATGAGAGA

ATTCCAGCACTGAAGTTGTTGGCAAGAGATAGTTTCTGTGGATGTTCTTCATCTGAAATTCTGAGGATGGAGAGAATTAT

TCTGGATAAGCTGAGCTGGGATCTTCACCCAGCCACACCACTGGATTTTCATCACATTTTCCATGCCATTGCAGTGTCAG

CTAGGCCTCAGTTACTTTTTAGTTTGCCAAACTGAGCTCATCTCAACATTTGGCTGTCCTCACCAAGCAACTACTTCACT

GTATGGCCTGCAACCAACTTCTGCAATTCAAAGGATCCATGCTTGCTCTGGCCATGATTAGTCTGGAAGTGGAGAAACTC

ATTCCTGATTGGCTTCCTCTTAGAATTGAACTGCTTCAGAAAGCACAGATGGATAGCTCCCAGCTGACCCGCTGTCGGGA

GCCATGGCACATCACCTTTCTACTCTGCAGTCCTCCCTGCCTCTAAATTCTGTTTATGTCTACTGTTCCCTCAAGCATGC

CCTGGTGACCTGTGACAAAGGAGTGTTCAGATTACATCCCTCCTCTGCCCCAGGCCCAGAGTTCTCCAAGGACAACAGCA

AACCAGAAGTGCCAGTCAGAGGTCCAGCGCCTTCTACCATCATCTCCCAGCTCGAATGGGTGCAAGCATACCTCTGCTGA

ATGCAAAGTAGAGGAAATGAAAGTGAACACCTTCTACGATGAGATCAAATGGCTCTGTAATGAAGATAATGCTTCAGAAA

ATGTGCGTTCTGTGTATGGCACTGATTTATCAAGGCAAGAGGGACATGCTTCCTTTGTCTACCTTTGCAGCCTGTTTCTG

TCATG

ORF - retro_vpac_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	87.32 %
Parental protein coverage:	92.84 %
Number of stop codons detected:	0
Number of frameshifts detected:	5

Retrocopy - Parental Gene Alignment:

                                ParentalKVNVPKMPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALASSLLDRFLATVKAHPKYLSCIAISCFFL
.VNVPKMPTNQNVSPS.RDEVIQWLAKLKYQF.LYPET.ALASSLL.RFLATVKAHPK.LSC.AI.CFFL
RetrocopyQVNVPKMPTNQNVSPSRRDEVIQWLAKLKYQFSLYPETYALASSLLHRFLATVKAHPKHLSCSAIECFFL
ParentalAAKTVEEDERIPGLKVLARDSFCGCSSSEILRMERIILDKLNWDLHTATPLDFLHIFHAIAVSTRPQLLF
AAKTVEEDERIP.LK.LARDSFCGCSSSEILRMERIILDKL.WDLH.ATPLDF.HIFHAIAVS.RPQLLF
RetrocopyAAKTVEEDERIPALKLLARDSFCGCSSSEILRMERIILDKLSWDLHPATPLDFHHIFHAIAVSARPQLLF
ParentalSLP-KLSPSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEMEKLIPDWLPLTIELLQKAQMDSSQL
SLP.KLS.SQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLE.EKLIPDWLPL.IELLQKAQMDSSQL
RetrocopySLP<KLSSSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEVEKLIPDWLPLRIELLQKAQMDSSQL
ParentalIHCRE-LVAHHLSTLQSSLPLNSVYVYRPLKHTLVTCDKGVFRLHPSSAPGPDFSKDNSKPEVPVRGTA-
..CRE...AHHLSTLQSSLPLNSVYVY..LKH.LVTCDKGVFRLHPSSAPGP.FSKDNSKPEVPVRG.A.
RetrocopyTRCRE<AMAHHLSTLQSSLPLNSVYVYCSLKHALVTCDKGVFRLHPSSAPGPEFSKDNSKPEVPVRGPA<
ParentalAFCHHLPA-ANGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDNASENVGSVCGTDLSRQEGHAS-PCPPLQ
AF.HHLPA..NGCKHTSA..KVEEM.V..FYD.IK.L.NEDNASENV.SV.GTDLSRQEGHAS..C.PLQ
RetrocopyAFYHHLPA<SNGCKHTSAECKVEEMKVNTFYDEIKWLCNEDNASENVRSVYGTDLSRQEGHAS<LCLPLQ
ParentalPVSVM
PVSVM
RetrocopyPVSVM

                            

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

                        

RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_197 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_197 was not experimentally validated.

Retrocopy orthology:

Vicugna pacos 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197 ,

	RetrogeneDB ID:	retro_vpac_197
Retrocopy location	Organism:	*Alpaca (Vicugna pacos)*
	Coordinates:	GeneScaffold_2739:169599..170644(+)
	Located in intron of:	ENSVPAG00000002872
Retrocopy information	Ensembl ID:	ENSVPAG00000002879
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	CCNI
	Ensembl ID:	ENSVPAG00000011865
	Aliases:	None
	Description:	cyclin I [Source:HGNC Symbol;Acc:1595]

Parental	KVNVPKMPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALASSLLDRFLATVKAHPKYLSCIAISCFFL
	.VNVPKMPTNQNVSPS.RDEVIQWLAKLKYQF.LYPET.ALASSLL.RFLATVKAHPK.LSC.AI.CFFL
Retrocopy	QVNVPKMPTNQNVSPSRRDEVIQWLAKLKYQFSLYPETYALASSLLHRFLATVKAHPKHLSCSAIECFFL

Parental	AAKTVEEDERIPGLKVLARDSFCGCSSSEILRMERIILDKLNWDLHTATPLDFLHIFHAIAVSTRPQLLF
	AAKTVEEDERIP.LK.LARDSFCGCSSSEILRMERIILDKL.WDLH.ATPLDF.HIFHAIAVS.RPQLLF
Retrocopy	AAKTVEEDERIPALKLLARDSFCGCSSSEILRMERIILDKLSWDLHPATPLDFHHIFHAIAVSARPQLLF

Parental	SLP-KLSPSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEMEKLIPDWLPLTIELLQKAQMDSSQL
	SLP.KLS.SQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLE.EKLIPDWLPL.IELLQKAQMDSSQL
Retrocopy	SLP<KLSSSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEVEKLIPDWLPLRIELLQKAQMDSSQL

Parental	IHCRE-LVAHHLSTLQSSLPLNSVYVYRPLKHTLVTCDKGVFRLHPSSAPGPDFSKDNSKPEVPVRGTA-
	..CRE...AHHLSTLQSSLPLNSVYVY..LKH.LVTCDKGVFRLHPSSAPGP.FSKDNSKPEVPVRG.A.
Retrocopy	TRCRE<AMAHHLSTLQSSLPLNSVYVYCSLKHALVTCDKGVFRLHPSSAPGPEFSKDNSKPEVPVRGPA<

Parental	AFCHHLPA-ANGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDNASENVGSVCGTDLSRQEGHAS-PCPPLQ
	AF.HHLPA..NGCKHTSA..KVEEM.V..FYD.IK.L.NEDNASENV.SV.GTDLSRQEGHAS..C.PLQ
Retrocopy	AFYHHLPA<SNGCKHTSAECKVEEMKVNTFYDEIKWLCNEDNASENVRSVYGTDLSRQEGHAS<LCLPLQ

Parental	PVSVM
	PVSVM
Retrocopy	PVSVM

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

RetrogeneDB ID:

retro_vpac_197