RetrogeneDB - Retrocopy retro_itri

						
>retro_itri_429
GCAATATCCCCTGGTTTGTGTGCTGTGGAAAGAGAAGAAGACTGTATAATCTTCTCAGAAGGAATAGTTGAGGAATACCT

AGCTTTCGACAATACAGATATGGAAGAGAGATTTCATGAAAATAAATCAGAAGCAGCTACAAAGAAACAGAAATTAGGGT

ACCCTCCCATTGCTCCATTTTACTCCATGAAAGAGGAAATTCTTGCTTATGTGTTTCGCAAAGTGTGGAGCAAAACTGTG

AGCTGTTTGGAGCAATTGACACGTAGTTACCGGGAAGGATTTGCTTCTGATGATGAGAGTAATGTTGCAGTCACCAGACC

AGATTCAGAAAGTCTCTATGTGCTGAGTGAACCACATACTTTGGTGTTACCTCCAGTGCCACAGTCCAAGGTGCTATCTG

TCACCTCGGATCTGATGAGTCTCTGTCAAGCAAGTGGTCATCAGCCAAATGCGAATGGTCTCTTGATTCATGGGATGCCT

CTAAAGCCAAGAAATCTCTACCCAATTGACAAGCTCCTAGATCTTGATGACAAGCTACTTATGAGGCCTGGGTCCAGTAC

CATTTTTTCAACCTGAAATTGGCCAAACCAAGCCTTGGAGCTTAGTACATCATGTCTGTCATATATAAAGTGCAGTCTGC

CAGGAGACGTAATCCCCCACCACGTACCCTTCATCCAATCAGCACAAGCCACTCACGCACTGGAACACCAAGACCTGTGG

AAGAAATCCTCAGAGGATCACAAGTCCCTTTGGCAGTTGACTGGCTCTCCTCTCGCTCACCAATACCCCTGAGTCGAAAT

AATCTGCTGCCACCTATTGGCACAAGCGAAGTGGAACACCTGAGCCCTGTGGAGCCACAAAGGCAAATGAAACCCCATGG

TGATTCCAGTCGAGCCCGAAGTGCAGTGGTGGATGAGCCTAACCATCAACAGCCTCAAGATAGGCTCCTTTTATCTAACT

TCTTCTCCAGGCCCAATACAACTCGGTCATTTATGCCAGAAACACAGTATCATCGTTCACATGCACTTGAATACCCTCAT

CAAGCCCGACCCAGTAGGTGATCTGCAGGTCCTCATTTGCATGCCTCTACAAAAATCTCAAAGCAGAGGTGGCCAATCTC

TAAAACCAGGCAGGGACCA

ORF - retro_itri_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	89.32 %
Parental protein coverage:	65.29 %
Number of stop codons detected:	2
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalARSPGLCAVEREEDCTIFSEGIIEEYLAFDHTDMEEGFHENKSEAATKKQKLGYPPIAPFYCIKEDILAY
		A.SPGLCAVEREEDC.IFSEGI.EEYLAFD.TDMEE.FHENKSEAATKKQKLGYPPIAPFY..KE.ILAY
RetrocopyAISPGLCAVEREEDCIIFSEGIVEEYLAFDNTDMEERFHENKSEAATKKQKLGYPPIAPFYSMKEEILAY
ParentalVFDNVWSKIVSCLAQLTRSHWEGFASDDESNVAVTRPDSESPYVLSEPHTLVLPPVPQSKVLSVTSNLMS
		VF..VWSK.VSCL.QLTRS..EGFASDDESNVAVTRPDSES.YVLSEPHTLVLPPVPQSKVLSVTS.LMS
RetrocopyVFRKVWSKTVSCLEQLTRSYREGFASDDESNVAVTRPDSESLYVLSEPHTLVLPPVPQSKVLSVTSDLMS
ParentalLCQASGHQPNANGLLIHGMPLQPRNLYLIDKLLDLDDKLLMRPGSSTIFSTRNWPNRALELSTSCLSYKV
		LCQASGHQPNANGLLIHGMPL.PRNLY.IDKLLDLDDKLLMRPGSSTIFST.NWPN.ALELSTSCLSY..
RetrocopyLCQASGHQPNANGLLIHGMPLKPRNLYPIDKLLDLDDKLLMRPGSSTIFST*NWPNQALELSTSCLSYIK
ParentalQS-ARRRNPP-PRTLHPISTSHSCTGTPRPVEEILRGSQVPLAVVDSLSSPSPIPLSRNNLLPPIGTSEV
		.S...RR..P.PRTLHPISTSHS.TGTPRPVEEILRGSQVPLA.VD.LSS.SPIPLSRNNLLPPIGTSEV
RetrocopyCS<SARRRNPPPRTLHPISTSHSRTGTPRPVEEILRGSQVPLA-VDWLSSRSPIPLSRNNLLPPIGTSEV
ParentalEHLSPVGPQRQMKPHGDSSRARSAVVDEPNYQQPQDRLLLSNFFSRPNTTQSFMPETQYHRSHALEYPHQ
		EHLSPV.PQRQMKPHGDSSRARSAVVDEPN.QQPQDRLLLSNFFSRPNTT.SFMPETQYHRSHALEYPHQ
RetrocopyEHLSPVEPQRQMKPHGDSSRARSAVVDEPNHQQPQDRLLLSNFFSRPNTTRSFMPETQYHRSHALEYPHQ
ParentalTRPSRGSAGSHLHAS-QKSQSRGG-PISKTRQGP
		.RPSR.SAG.HLHAS.QKSQSRGG.PISKTRQGP
RetrocopyARPSR*SAGPHLHAS>QKSQSRGG<PISKTRQGP

							

							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_429 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_429 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429 ,

	RetrogeneDB ID:	retro_itri_429
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393291.1:3482172..3483311(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM149B1
	Ensembl ID:	ENSSTOG00000002142
	Aliases:	None
	Description:	family with sequence similarity 149, member B1 [Source:HGNC Symbol;Acc:29162]

Parental	ARSPGLCAVEREEDCTIFSEGIIEEYLAFDHTDMEEGFHENKSEAATKKQKLGYPPIAPFYCIKEDILAY
	A.SPGLCAVEREEDC.IFSEGI.EEYLAFD.TDMEE.FHENKSEAATKKQKLGYPPIAPFY..KE.ILAY
Retrocopy	AISPGLCAVEREEDCIIFSEGIVEEYLAFDNTDMEERFHENKSEAATKKQKLGYPPIAPFYSMKEEILAY

Parental	VFDNVWSKIVSCLAQLTRSHWEGFASDDESNVAVTRPDSESPYVLSEPHTLVLPPVPQSKVLSVTSNLMS
	VF..VWSK.VSCL.QLTRS..EGFASDDESNVAVTRPDSES.YVLSEPHTLVLPPVPQSKVLSVTS.LMS
Retrocopy	VFRKVWSKTVSCLEQLTRSYREGFASDDESNVAVTRPDSESLYVLSEPHTLVLPPVPQSKVLSVTSDLMS

Parental	LCQASGHQPNANGLLIHGMPLQPRNLYLIDKLLDLDDKLLMRPGSSTIFSTRNWPNRALELSTSCLSYKV
	LCQASGHQPNANGLLIHGMPL.PRNLY.IDKLLDLDDKLLMRPGSSTIFST.NWPN.ALELSTSCLSY..
Retrocopy	LCQASGHQPNANGLLIHGMPLKPRNLYPIDKLLDLDDKLLMRPGSSTIFST*NWPNQALELSTSCLSYIK

Parental	QS-ARRRNPP-PRTLHPISTSHSCTGTPRPVEEILRGSQVPLAVVDSLSSPSPIPLSRNNLLPPIGTSEV
	.S...RR..P.PRTLHPISTSHS.TGTPRPVEEILRGSQVPLA.VD.LSS.SPIPLSRNNLLPPIGTSEV
Retrocopy	CS<SARRRNPPPRTLHPISTSHSRTGTPRPVEEILRGSQVPLA-VDWLSSRSPIPLSRNNLLPPIGTSEV

Parental	EHLSPVGPQRQMKPHGDSSRARSAVVDEPNYQQPQDRLLLSNFFSRPNTTQSFMPETQYHRSHALEYPHQ
	EHLSPV.PQRQMKPHGDSSRARSAVVDEPN.QQPQDRLLLSNFFSRPNTT.SFMPETQYHRSHALEYPHQ
Retrocopy	EHLSPVEPQRQMKPHGDSSRARSAVVDEPNHQQPQDRLLLSNFFSRPNTTRSFMPETQYHRSHALEYPHQ

Parental	TRPSRGSAGSHLHAS-QKSQSRGG-PISKTRQGP
	.RPSR.SAG.HLHAS.QKSQSRGG.PISKTRQGP
Retrocopy	ARPSR*SAGPHLHAS>QKSQSRGG<PISKTRQGP

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

RetrogeneDB ID:

retro_itri_429