RetrogeneDB - Retrocopy retro_tsyr

						
>retro_tsyr_1983
ATGCAGCCCACAACCTGCCCTCTCAATTTGACCCTGAAAGTAGAGGAAGAAGAGATTCAGAGCCAGGAACTGGAGGATGG

CCCCGGGGGATATGCAGAAAGTACGGATCTGCTCAGAGGGCGGATGGGTGCCGGCCCTGTTTGATGAGGTGGCCATGTAT

GTTTCCGATGAGGAGTGAGAAGTTTTGACGGAGCAACAAAAGGCCCTCTACCGGGAAGTCATGAGGATGAATTATGAAAC

TGTCTTTTCCCTGGAATTCCCACTTCCTAAGCCAGACATCATCACCCGACTGGAAGGGGAGGAGGAGTCTCAGAATTCTG

ACGAGAGGCAGCTCCAGGGCGACACCTTTGCAGACACTGCGAAAAATGAAGGGTCTGATGTGAAGCCTTCAGAGTGGGCG

AGCCCAGTGAACCCCACCTCGCAGTTTCCTCAGCCTCAGCACCTAGACAGCTTCGGTCTCCGTTTGCCTCGAGACATCAC

GGAGCTGCCCGAGGGGAGTGAAGGGTACCCCTTCTACATGGCAGTGGGCTTGCCAGGGTATGATCTCTCGGCTGACGACA

TAGCTGGAAAATTCCAGTTCAGCCGGGGCATGTGCCACAGTTGCGATGCAGGCTTCCAGCTCATGGTGGTAGAGTACGCC

AAGAGCACCAATTGCCAAGCTGCCAAGCAGTTTGGGGTGTTGGAGAAAAACGTTATAGACTGGCGCAAGGTGAAGCCGCA

GTTCCAGAATGCCTATGCCATGAGGCGGGCATTCCGGGGCCCCAAGAATGGCAGGTTTGCTCTGGTGGACCAGCGTGTGG

CCGCATACGTCAGATACATGCAGGTCAAAGGGGACTCCATCACCAGGGAGGCTATGCGGCTGAAGGCTCGCCAAATCCCC

CAGGAGATGAACATTCCAGAGAAAGCATTCAAGGCAAGCTTGGGTTGGTGCCGAAGAATGATGAGAAGGTGTGACCTGTC

TCTGAGACATAAAGGGCCAGTGCCTCAGCACCTGCCAGACGACCTGAGAAGCTCCTCACTTACCAGCGGAGCATTCTGGC

TCTGCCTAAGGCGC

ORF - retro_tsyr_1983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	81.41 %
Parental protein coverage:	57.64 %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMESTTYPLNLNLKVEEEEEEIQSRELEDGPA-DMQKVRXXXXXXXVPALFDEVAIYFSDEEWEVLTEQQK
		M..TT.PLNL.LKVEEEE..IQS.ELEDGP..DMQKVR.......VPALFDEVA.Y.SDEE.EVLTEQQK
RetrocopyMQPTTCPLNLTLKVEEEE--IQSQELEDGPG>DMQKVRICSEGGWVPALFDEVAMYVSDEE*EVLTEQQK
ParentalALYREVMRMNYETVLSLEFPFPKPDMITRLEGEEESQNSDEWQLHGGTFAE---NEESDVKPSEWASPVN
		ALYREVMRMNYETV.SLEFP.PKPD.ITRLEGEEESQNSDE.QL.G.TFA....NE.SDVKPSEWASPVN
RetrocopyALYREVMRMNYETVFSLEFPLPKPDIITRLEGEEESQNSDERQLQGDTFADTAKNEGSDVKPSEWASPVN
ParentalPTSQFPQPQHLDSLGLRLPRDIAELPEWSEGYPFYMAMGFPGYDLSADDIAGKFQFSRGMRRSYDAGFKL
		PTSQFPQPQHLDS.GLRLPRDI.ELPE.SEGYPFYMA.G.PGYDLSADDIAGKFQFSRGM..S.DAGF.L
RetrocopyPTSQFPQPQHLDSFGLRLPRDITELPEGSEGYPFYMAVGLPGYDLSADDIAGKFQFSRGMCHSCDAGFQL
ParentalMVVEYAESTNNCQAAKQFGVLEKNVRDWRKVKPQLQNAHAMRRAFRGPKNGRFALVDQRVAEYVRYMQAK
		MVVEYA.STN.CQAAKQFGVLEKNV.DWRKVKPQ.QNA.AMRRAFRGPKNGRFALVDQRVA.YVRYMQ.K
RetrocopyMVVEYAKSTN-CQAAKQFGVLEKNVIDWRKVKPQFQNAYAMRRAFRGPKNGRFALVDQRVAAYVRYMQVK
ParentalGDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLRHKVPVPQHLPEDLTEKLVTYQRSV
		GD.ITREAM.LKA..I.QEMNIPEK.FKASLGWCRRMMRR.DLSLRHK.PVPQHLP.DL.....T.....
RetrocopyGDSITREAMRLKARQIPQEMNIPEKAFKASLGWCRRMMRRCDLSLRHKGPVPQHLPDDLRSSSLTSGAFW
ParentalLALRR
		L.LRR
RetrocopyLCLRR

							

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

						

RNA-Seq - click to see more details

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tarsius syrichta was not studied using ChIP-Seq data.

EST - click to see more details

Tarsius syrichta was not studied using EST data.

TSS - click to see more details

Tarsius syrichta was not studied using FANTOM5 data.

Lab - click to see more details

retro_tsyr_1983 was not experimentally validated.

Retrocopy orthology:

Tarsius syrichta 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983 ,

	RetrogeneDB ID:	retro_tsyr_1983
Retrocopy location	Organism:	*Tarsier (Tarsius syrichta)*
	Coordinates:	scaffold_74948:3584..4638(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	POGK
	Ensembl ID:	ENSTSYG00000011078
	Aliases:	None
	Description:	pogo transposable element with KRAB domain [Source:HGNC Symbol;Acc:18800]

Parental	MESTTYPLNLNLKVEEEEEEIQSRELEDGPA-DMQKVRXXXXXXXVPALFDEVAIYFSDEEWEVLTEQQK
	M..TT.PLNL.LKVEEEE..IQS.ELEDGP..DMQKVR.......VPALFDEVA.Y.SDEE.EVLTEQQK
Retrocopy	MQPTTCPLNLTLKVEEEE--IQSQELEDGPG>DMQKVRICSEGGWVPALFDEVAMYVSDEE*EVLTEQQK

Parental	ALYREVMRMNYETVLSLEFPFPKPDMITRLEGEEESQNSDEWQLHGGTFAE---NEESDVKPSEWASPVN
	ALYREVMRMNYETV.SLEFP.PKPD.ITRLEGEEESQNSDE.QL.G.TFA....NE.SDVKPSEWASPVN
Retrocopy	ALYREVMRMNYETVFSLEFPLPKPDIITRLEGEEESQNSDERQLQGDTFADTAKNEGSDVKPSEWASPVN

Parental	PTSQFPQPQHLDSLGLRLPRDIAELPEWSEGYPFYMAMGFPGYDLSADDIAGKFQFSRGMRRSYDAGFKL
	PTSQFPQPQHLDS.GLRLPRDI.ELPE.SEGYPFYMA.G.PGYDLSADDIAGKFQFSRGM..S.DAGF.L
Retrocopy	PTSQFPQPQHLDSFGLRLPRDITELPEGSEGYPFYMAVGLPGYDLSADDIAGKFQFSRGMCHSCDAGFQL

Parental	MVVEYAESTNNCQAAKQFGVLEKNVRDWRKVKPQLQNAHAMRRAFRGPKNGRFALVDQRVAEYVRYMQAK
	MVVEYA.STN.CQAAKQFGVLEKNV.DWRKVKPQ.QNA.AMRRAFRGPKNGRFALVDQRVA.YVRYMQ.K
Retrocopy	MVVEYAKSTN-CQAAKQFGVLEKNVIDWRKVKPQFQNAYAMRRAFRGPKNGRFALVDQRVAAYVRYMQVK

Parental	GDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLRHKVPVPQHLPEDLTEKLVTYQRSV
	GD.ITREAM.LKA..I.QEMNIPEK.FKASLGWCRRMMRR.DLSLRHK.PVPQHLP.DL.....T.....
Retrocopy	GDSITREAMRLKARQIPQEMNIPEKAFKASLGWCRRMMRRCDLSLRHKGPVPQHLPDDLRSSSLTSGAFW

Parental	LALRR
	L.LRR
Retrocopy	LCLRR

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

RetrogeneDB ID:

retro_tsyr_1983