RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_137
ATGGAGGAGCAGCCGAAGGAGGGCGAGGCCGAGGTCGCGGAGCACTGGTTCTCCAAGTGGGAGCGCCAGTGCTTGGACGA

GGCCGAGCAGGACGAGCAGCTGCCCCCAGAGCTGCAGGAGGAGGCAGCCGCCGAGGCGGCTGGGCTCAAGAGCGAGCAGC

AGAGGCTCTGGCACCTCTTCCAGATCTCAGCCACCGCGGTGGCCCAGCTCTACAAAGATTCTGGGTGCCAACAGCCAGGA

CTGTCTATGTGGGACCCCTTCCAGAATGCAGCCATGGCCGTGACCAGCCTCTACAAAGAGAGTGGGGATGCCCACCAACG

AAGTTTTGACCTGGGAGTCCAGGTTGGCTACCAGCGTCGCATCAAAGATGTGCTGGAGTGGGTGAAGAAGGGCCGGAGCA

CCATTCGCCGCGAAGACCTGATTAGCTTCCTATGTGGCAAAGTGCCCCCTGCCCCTCCCCCGCCACGCACCTCTAGGATG

CCCCCGAAGCCACCCTCTGGGGCCGCTAGCCAAGCTGGGGCAACCGAGTCCAGCTCTTCGGTTGACGTCGACCTGCAGCC

TTTCCATGAGGCCATTGCCCTGCATGGCCTCAATGGCGCCATGGCAAGCATCAGTGTGCGATCTGGCGCGCCTGGTTCCC

CGCCTCAAGACAGCGGTGTGGCCAGCAGTGGACGACGAAAAAGTAGTTTCCTCGAGGATGACCTGAACCCCTTTGGCTCC

GAAGAACTAGCCCTCTGCCTGGACAGTGGGGGGATCCGCAAGCGCACTTCGGCCCAGTTCGGTGATGGCATCACAGACTC

CCCGTCCCACAAGCGCAACCGAATGGTCTAA

ORF - retro_itri_137 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	68.14 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLIS
D..CQQPGLS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.GYQRR.KDVL.WVKK.R.TIRREDLIS
RetrocopyDSGCQQPGLSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGYQRRIKDVLEWVKKGRSTIRREDLIS
ParentalFLCGKV----PPPRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPG
FLCGKV....PPPR.SR.PP.........A..TE.SSSV..DLQPF.EAIALHGL.GAMASISVRS..PG
RetrocopyFLCGKVPPAPPPPRTSRMPPKPPSGAASQAGATESSSSVDVDLQPFHEAIALHGLNGAMASISVRSGAPG
ParentalSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
SP...S......RR.......DLN.F.SEE.AL.LD.GG.RKRTSAQ.GD.ITDSP.HKRNRM.
RetrocopySPPQDSGVASSGRRKSSFLEDDLNPFGSEELALCLDSGGIRKRTSAQFGDGITDSPSHKRNRMV

                            

                            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_137 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_137 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 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137 ,

	RetrogeneDB ID:	retro_itri_137
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393323.1:7551396..7552227(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSSTOG00000027606
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	C16orf72
	Ensembl ID:	ENSSTOG00000009324
	Aliases:	None
	Description:	chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]

Parental	DRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLIS
	D..CQQPGLS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.GYQRR.KDVL.WVKK.R.TIRREDLIS
Retrocopy	DSGCQQPGLSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGYQRRIKDVLEWVKKGRSTIRREDLIS

Parental	FLCGKV----PPPRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPG
	FLCGKV....PPPR.SR.PP.........A..TE.SSSV..DLQPF.EAIALHGL.GAMASISVRS..PG
Retrocopy	FLCGKVPPAPPPPRTSRMPPKPPSGAASQAGATESSSSVDVDLQPFHEAIALHGLNGAMASISVRSGAPG

Parental	SPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
	SP...S......RR.......DLN.F.SEE.AL.LD.GG.RKRTSAQ.GD.ITDSP.HKRNRM.
Retrocopy	SPPQDSGVASSGRRKSSFLEDDLNPFGSEELALCLDSGGIRKRTSAQFGDGITDSPSHKRNRMV

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

RetrogeneDB ID:

retro_itri_137