RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_352
GGCTGCAGGCAGCCACATTATGTCCTCGTCACAATCTCCAGCCCCTGCTGCCTCAGTACCTCTGCTATTTCATTTGCAGA

AGCCCAGGTCCAAGTACCTCCTGTTGTTCCTGCAACTCCTTCACCCACAGCAGTACCTGAGGTGGCTTCTGGAAGAACTA

CAGATGTAATCCAAGCTGTTGCAGAACAGAGCTTCGCTGAACTGGGACTAGGGTCATACACCCCAGTGGGATTGATCCAG

AACCTCCTGGAATTTATGCATGTTAACCTGGGCCTTCCTTGGTGGGGGGCCATTGCAGCATGTACAGTCCTTGCCCACTG

CCTCGTTTTTTCCTCTCATCGTAAAGGGCCAGCAAGAGGTAGCCAAGATTCACAACCACTTGCCAGAGATCCGGAAGTTT

TCCACTAGAATCAGAGAGGCCAAGTTGGCAGGAGACAATGCTGAGTTTCACAGGGCCTCCAAGGAGATGACACTTTACCA

GAAAAAGCAAGATATTAAATTCTTTAAACCCCTCATTCTGCCTCTGACTCAGGCACTAGTCTTCATCTCCTTCTTCATTG

CCTTGAGAGAGATGGCCAACCTTCCTGTGCTCAGTATGCAGACAGGTGGCCTCTGGTGGTTCCAGGATCTCACTGTATCT

GATCCCATCTACATGTTACCGATAGTAGTCACTGCTACAATGTGGGGTGTCCTGGAGCTAGGTGCTGACACAGGTGTGCA

AAGTTCTGACCTTCAGTGGATGAGAAATGTTATCAGAGTGATGCCCCTGGCAGTCTTGCCCATAACCATCCACTTCCCCT

CGGCAGTGTTCATGTACTGGCTCTCCTCCAATATGTTTTCCCTGGGCCAAGTAGCCTGCCTCTGACTACTGTACACACTG

TACTTAAAATACCCCAGCGTGTTGTGCATGACCCTGACAAATTATCTCCCCGGGAAGGCTTCATAAAGAGCTTCAAACAA

GGCTGGAAGAATGCTGAAATTGCACATCAGCTCCATGAGCGTGAACGACGCATGCAGAACCACTTGGAGCTAGCAGCCAG

GGGTCCCTTACAGCAGACCTTTACCCACAGCCCTCTACTACAACATGAAAAGAATCACCCTCCCAAA

ORF - retro_itri_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.67 %
Parental protein coverage:	96.61 %
Number of stop codons detected:	1
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalGCRQPHYVLLTTSSHRCLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASGGTTDTIQAVAEQSFAELGL
GCRQPHYVL.T.SS..CLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASG.TTD.IQAVAEQSFAELGL
RetrocopyGCRQPHYVLVTISSPCCLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASGRTTDVIQAVAEQSFAELGL
ParentalGSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLARCLVF-PLIVKGQREAAKIHNHLPEIQKFSTRIRE
GSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLA.CLVF.PLIVKGQ.E.AKIHNHLPEI.KFSTRIRE
RetrocopyGSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLAHCLVF>PLIVKGQQEVAKIHNHLPEIRKFSTRIRE
ParentalAKLAGDNAEFYRASSEMTLYQKKHDIKFFKPLILPLTQAPVFISFFIALREMANLPVPSMQTGGLWWFQD
AKLAGDNAEF.RAS.EMTLYQKK.DIKFFKPLILPLTQA.VFISFFIALREMANLPV.SMQTGGLWWFQD
RetrocopyAKLAGDNAEFHRASKEMTLYQKKQDIKFFKPLILPLTQALVFISFFIALREMANLPVLSMQTGGLWWFQD
ParentalLTISDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF
LT.SDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF
RetrocopyLTVSDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF
ParentalSLGQVACLRIPAVRTVLKIP-QRVVHDPDKLPPREGFIKSFKQGWKNAEIAHQLRERERRMQNHLELAAR
SLGQVACL........LK.P.QRVVHDPDKL.PREGFIKSFKQGWKNAEIAHQL.ERERRMQNHLELAAR
RetrocopySLGQVACL*L-LYTLYLKYP<QRVVHDPDKLSPREGFIKSFKQGWKNAEIAHQLHERERRMQNHLELAAR
ParentalGPLRQTFTHNPLLQHEKNHPPK
GPL.QTFTH.PLLQHEKNHPPK
RetrocopyGPLQQTFTHSPLLQHEKNHPPK

                            

                            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_352 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_352 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012893	1 retrocopy	retro_mluc_2461,
Monodelphis domestica	ENSMODG00000005347	1 retrocopy	retro_mdom_1308,
Oryctolagus cuniculus	ENSOCUG00000000720	1 retrocopy	retro_ocun_367,
Otolemur garnettii	ENSOGAG00000000631	1 retrocopy	retro_ogar_2369,
Ictidomys tridecemlineatus	ENSSTOG00000003318	1 retrocopy	retro_itri_352 ,

	RetrogeneDB ID:	retro_itri_352
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393285.1:22207384..22208491(-)
	Located in intron of:	ENSSTOG00000003062
Retrocopy information	Ensembl ID:	ENSSTOG00000022167
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	OXA1L
	Ensembl ID:	ENSSTOG00000003318
	Aliases:	None
	Description:	oxidase (cytochrome c) assembly 1-like [Source:HGNC Symbol;Acc:8526]

Parental	GCRQPHYVLLTTSSHRCLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASGGTTDTIQAVAEQSFAELGL
	GCRQPHYVL.T.SS..CLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASG.TTD.IQAVAEQSFAELGL
Retrocopy	GCRQPHYVLVTISSPCCLSTSAISFAEAQVQVPPVVPATPSPTAVPEVASGRTTDVIQAVAEQSFAELGL

Parental	GSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLARCLVF-PLIVKGQREAAKIHNHLPEIQKFSTRIRE
	GSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLA.CLVF.PLIVKGQ.E.AKIHNHLPEI.KFSTRIRE
Retrocopy	GSYTPVGLIQNLLEFMHVNLGLPWWGAIAACTVLAHCLVF>PLIVKGQQEVAKIHNHLPEIRKFSTRIRE

Parental	AKLAGDNAEFYRASSEMTLYQKKHDIKFFKPLILPLTQAPVFISFFIALREMANLPVPSMQTGGLWWFQD
	AKLAGDNAEF.RAS.EMTLYQKK.DIKFFKPLILPLTQA.VFISFFIALREMANLPV.SMQTGGLWWFQD
Retrocopy	AKLAGDNAEFHRASKEMTLYQKKQDIKFFKPLILPLTQALVFISFFIALREMANLPVLSMQTGGLWWFQD

Parental	LTISDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF
	LT.SDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF
Retrocopy	LTVSDPIYMLPIVVTATMWGVLELGADTGVQSSDLQWMRNVIRVMPLAVLPITIHFPSAVFMYWLSSNMF

Parental	SLGQVACLRIPAVRTVLKIP-QRVVHDPDKLPPREGFIKSFKQGWKNAEIAHQLRERERRMQNHLELAAR
	SLGQVACL........LK.P.QRVVHDPDKL.PREGFIKSFKQGWKNAEIAHQL.ERERRMQNHLELAAR
Retrocopy	SLGQVACL*L-LYTLYLKYP<QRVVHDPDKLSPREGFIKSFKQGWKNAEIAHQLHERERRMQNHLELAAR

Parental	GPLRQTFTHNPLLQHEKNHPPK
	GPL.QTFTH.PLLQHEKNHPPK
Retrocopy	GPLQQTFTHSPLLQHEKNHPPK

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

RetrogeneDB ID:

retro_itri_352