RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_673
GTAGAGAGAGAAACGAGGAAAGATGAGTTACTGGATATTGCCAAGTCAAAACAAGAATGTACAAATTCAGAACTGCATAA

TTTGAGACAGATTTATGTAAAAATAACAGAGTTATCTGCAGTTTTTTAGTTTCAATGTGGAAAATTCTCCGGAATTAACA

CAAATATATACTTCAAAGATTGAGAAATTGAAGGCCCTGTCATCCAGTATAGACATATGTTTATCAGACCTTGACAAAAA

CCACCTAAAAGTTGATGCTAAGAGGGAGAAAAATCAGAAGTCACTGGTTAAGGACCCAAAATCTGAGACTACATTGGCTC

AGTAAAATAGGCCAGACAAGATTTCTTGTGAGGTATGCAAAGGAAAGAAACTACAGATTAATACTGAATTGGGAAAAAAT

GTATAATTGTTTTCTCATCTCTGTTTATAAATACTTAATGGAGAAATAAAAGTCTTGGTCTCTGGGTGGAAAAATCCAGA

GTGAACCAAAAAAAAAAAATCACAATGTGCAAGATCCAAGAAACATCACCAAAAGGTGGTGGAATTAGGTTTCAGAATGA

AGAGAAGCAGCTCTCGGACACTTTCACATCTTTACCTGATGTAAAGCAGTGGCATGATGTCAATGTTTACCTAGGCCTGG

CCAACTGTTCTGATTCAAAGCCACCTGAAAAGCTGAATGTGGACTGTCATGACCTTATGGAAAGTTCTGAGATTTCATGT

GGCCCCAGGAATGAAGGATGTCAGGATGGCAGAGACCCATGTGAATCCAAGTGCTGCTACTCGAGTAACTTCATAATCGA

AGACCCAGGTCACATGTCTGATATGGAATGGATGAGTATTTTCAATCCTTCTAAAATGCTAAGAATTACTCACCATAAAT

CTGTGTGCACTTGTTCAGGAAGTGTCAGTGCCACAAAATATAACTCCTCTATAAGTAAGCTAATCTCCATCCAGCATTCC

CACTGTTTGAGTTCTCCAAAGTCTGTCCTAAGAAAGGATGAGACAGAGACCCCTCCTGATAAAAATAATTTCTCCAAGGG

TTTGTTAATCAACAAAGATGCAGTATTTTCCAGC

ORF - retro_itri_673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.28 %
Parental protein coverage:	83.84 %
Number of stop codons detected:	2
Number of frameshifts detected:	4

Retrocopy - Parental Gene Alignment:

                                ParentalVEREKRKDELLDIAKSKQERTNSELHNLRQIYVKQ-QSDLQFLNFNVENSQELIQIYDSKIEESKALTSS
VERE.RKDELLDIAKSKQE.TNSELHNLRQIYVK..QS.LQF..FNVENS.EL.QIY.SKIE..KAL.SS
RetrocopyVERETRKDELLDIAKSKQECTNSELHNLRQIYVKI>QSYLQFFSFNVENSPELTQIYTSKIEKLKALSSS
ParentalRDMCLSDLDNNHLKVDAKREKSQKSLVKDPKFETTLAQQNRPDKISCEVCKGKKLQINTE-SGEKNIIAL
.D.CLSDLD.NHLKVDAKREK.QKSLVKDPK.ETTLAQ.NRPDKISCEVCKGKKLQINTE..G.K.II..
RetrocopyIDICLSDLDKNHLKVDAKREKNQKSLVKDPKSETTLAQ*NRPDKISCEVCKGKKLQINTE<IGKKCIIVF
ParentalSSLFT-KDLMEKQKSWSLGGKIQSE-PENKITLCKIHETSSKGGGIRFQNEEKQLWESSASLPDEKQWHD
SSLF..K.LMEK.KSWSLGGKIQSE......T.CKI.ETS.KGGGIRFQNEEKQL.....SLPD.KQWHD
RetrocopySSLFI<KYLMEK*KSWSLGGKIQSE>XXXXXTMCKIQETSPKGGGIRFQNEEKQLSDTFTSLPDVKQWHD
ParentalVSVYLGLTDCSDAKPPEKLDVDCHDLMEKSEMSCGPRNEGCQSDSDLYESKCCHPSNFIIEAPGHMSDME
V.VYLGL..CSD.KPPEKL.VDCHDLME.SE.SCGPRNEGCQ...D..ESKCC..SNFIIE.PGHMSDME
RetrocopyVNVYLGLANCSDSKPPEKLNVDCHDLMESSEISCGPRNEGCQDGRDPCESKCCYSSNFIIEDPGHMSDME
ParentalWMSIFKPSKVQRIVRHKSVCTCSGSVSATKYNSSASELIAIQHSHCLSSSKSALREDETEAPPDKNNLSK
WMSIF.PSK..RI..HKSVCTCSGSVSATKYNSS.S.LI.IQHSHCLSS.KS.LR.DETE.PPDKNN.SK
RetrocopyWMSIFNPSKMLRITHHKSVCTCSGSVSATKYNSSISKLISIQHSHCLSSPKSVLRKDETETPPDKNNFSK
ParentalGLLINKEAALSS
GLLINK.A..SS
RetrocopyGLLINKDAVFSS

                            

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

                        

RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_673 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_673 was not experimentally validated.

Retrocopy orthology:

Ictidomys tridecemlineatus 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011521	2 retrocopies	retro_chof_311, retro_chof_894,
Ictidomys tridecemlineatus	ENSSTOG00000014132	1 retrocopy	retro_itri_673 ,

	RetrogeneDB ID:	retro_itri_673
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393309.1:13576160..13577234(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CCDC62
	Ensembl ID:	ENSSTOG00000014132
	Aliases:	None
	Description:	coiled-coil domain containing 62 [Source:HGNC Symbol;Acc:30723]

Parental	VEREKRKDELLDIAKSKQERTNSELHNLRQIYVKQ-QSDLQFLNFNVENSQELIQIYDSKIEESKALTSS
	VERE.RKDELLDIAKSKQE.TNSELHNLRQIYVK..QS.LQF..FNVENS.EL.QIY.SKIE..KAL.SS
Retrocopy	VERETRKDELLDIAKSKQECTNSELHNLRQIYVKI>QSYLQFFSFNVENSPELTQIYTSKIEKLKALSSS

Parental	RDMCLSDLDNNHLKVDAKREKSQKSLVKDPKFETTLAQQNRPDKISCEVCKGKKLQINTE-SGEKNIIAL
	.D.CLSDLD.NHLKVDAKREK.QKSLVKDPK.ETTLAQ.NRPDKISCEVCKGKKLQINTE..G.K.II..
Retrocopy	IDICLSDLDKNHLKVDAKREKNQKSLVKDPKSETTLAQ*NRPDKISCEVCKGKKLQINTE<IGKKCIIVF

Parental	SSLFT-KDLMEKQKSWSLGGKIQSE-PENKITLCKIHETSSKGGGIRFQNEEKQLWESSASLPDEKQWHD
	SSLF..K.LMEK.KSWSLGGKIQSE......T.CKI.ETS.KGGGIRFQNEEKQL.....SLPD.KQWHD
Retrocopy	SSLFI<KYLMEK*KSWSLGGKIQSE>XXXXXTMCKIQETSPKGGGIRFQNEEKQLSDTFTSLPDVKQWHD

Parental	VSVYLGLTDCSDAKPPEKLDVDCHDLMEKSEMSCGPRNEGCQSDSDLYESKCCHPSNFIIEAPGHMSDME
	V.VYLGL..CSD.KPPEKL.VDCHDLME.SE.SCGPRNEGCQ...D..ESKCC..SNFIIE.PGHMSDME
Retrocopy	VNVYLGLANCSDSKPPEKLNVDCHDLMESSEISCGPRNEGCQDGRDPCESKCCYSSNFIIEDPGHMSDME

Parental	WMSIFKPSKVQRIVRHKSVCTCSGSVSATKYNSSASELIAIQHSHCLSSSKSALREDETEAPPDKNNLSK
	WMSIF.PSK..RI..HKSVCTCSGSVSATKYNSS.S.LI.IQHSHCLSS.KS.LR.DETE.PPDKNN.SK
Retrocopy	WMSIFNPSKMLRITHHKSVCTCSGSVSATKYNSSISKLISIQHSHCLSSPKSVLRKDETETPPDKNNFSK

Parental	GLLINKEAALSS
	GLLINK.A..SS
Retrocopy	GLLINKDAVFSS

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

RetrogeneDB ID:

retro_itri_673