RetrogeneDB - Retrocopy retro_ogar

                        
>retro_ogar_2862
CTGAATAACATCAAGCAGTTTAAGAAATATATTGATAGTCCTAAATTAAGGGAGCTTCTGATAATTGGAGGTGTTGCAGC

ACAGGACCAGCTCTCGGTTTTGGAAAATGGGGTAGATATAGTTGTAGGCACTCCAGGAAGAATGGATGACTTGATGTCAA

CTGGAAAACTGAACTTATCTCAAGTTAGATTTCTGGTCCTCCAAGAAGCTGATGGGCTGCTTTCTCAAGGTTAATCTGAC

TTTATAAATAGGATGCACAATCAGATTCCTCAGATTACCTCTGATGGAAAAAGACTTCAGGTGATTGTTTGCTCTGTCAC

TTTGCATTCTTTTAATGTAAAGAAATTATCTGAAAAGATAATGCATTTTCCTATGTGAGTTGATTTAAAAGAAGATTCTG

TTCCAGATACTGTACACCAAGTTGTTGTTCCAGTGAATCCCAAAACTGACAGACTCTGGGAAAGGCTTGGAATGAACCAC

ATTAGAACTGGTGATGTACATGCAAAGATAACACAAGACCTGATGCTAATAGTCTGGAAATGTAGTATGAAGCTGTTAAA

ATTCTGAAGGGGGGAGTATACTGTCTGGCAATCAAGGAACACAAAAAGGATCAAACAATTATCTTCTATAGAACCAAGAT

TGACTGTGATAACTTGGAGCAATATTTTGTGCAACAAGGAGGAGGACCTGATAAAAAGGGGCACCAGTTCTTATGTGTTT

ATCTTCATGGTGACAGAAAGTGTCATGAGAGAAAGAAAAACTTGGAAAGATTTAAGAAAGGAGATGTAAGATTCTGCACA

GATGTAGCTGCTAGCGGAATTGATATTCATGGTGTTCCTTATGTTACAAATGTCACTCTACCTGATGAAAAGCAAAACTA

CGTACATTGAATTGGCAGAGTAGGAAGAGCGGAAAGAATGGGTCTGGCCATTTCCCTGGTGGCATCAGAGAAAGAAAAGG

TTTGGTACCCTGTATGTAGCAGCCGTGGAAAGGAGTATTACAACACAAGACTCAAGGAAGACGGAGGCTGTACCATATGG

TACAATGAGATGCAGTTTACTATCTGAGAAAGAACACCTGAACTATACCATTTCTCAAGTTGAGCCAGATATAAAGGTAC

CAGTGGATGAATTTGATGGAAAAGTTACCTATGGTCAAAAAAGGGCTGCTGGTGGTGGAATTTATAAATGCCATGTGGAT

ATTTTGACACCTACCATTCAAGAGTTGGTTTCCCTTGAAAAAGAAGCACAGACTCGGCGCCTATAGCTCAACCGGCTAAG

ACGCCAG

ORF - retro_ogar_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.9 %
Parental protein coverage:	58.83 %
Number of stop codons detected:	5
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalLNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEA
LNNIKQFKKYID.PKLRELLIIGGVAA.DQLSVLENGVDIVVGTPGR.DDL.STGKLNLSQVRFLVL.EA
RetrocopyLNNIKQFKKYIDSPKLRELLIIGGVAAQDQLSVLENGVDIVVGTPGRMDDLMSTGKLNLSQVRFLVLQEA
ParentalDGLLSQGYSDFINRMHNQIPQITSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVH
DGLLSQG.SDFINRMHNQIPQITSDGKRLQVIVCS.TLHSF.VKKLSEKIMHFP..VDLK.EDSVPDTVH
RetrocopyDGLLSQG*SDFINRMHNQIPQITSDGKRLQVIVCSVTLHSFNVKKLSEKIMHFPM*VDLK-EDSVPDTVH
ParentalHVVVPVNPKTDRLWERLGKNHIRTDDVHA-KDNTRPGANSPEMWSEAVKILKGEYTVRAIKEHKMDQAII
.VVVPVNPKTDRLWERLG.NHIRT.DVHA.KDNTRP.ANS.EM..EAVKILKG.....AIKEHK.DQ.II
RetrocopyQVVVPVNPKTDRLWERLGMNHIRTGDVHA<KDNTRPDANSLEM*YEAVKILKGGVYCLAIKEHKKDQTII
ParentalFCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDI
F.RTKIDCDNLEQYF.QQGGGPDKKGHQF.CV.LHGDRK.HERK.NLERFKKGDVRF..CTDVAA.GIDI
RetrocopyFYRTKIDCDNLEQYFVQQGGGPDKKGHQFLCVYLHGDRKCHERKKNLERFKKGDVRF--CTDVAASGIDI
ParentalHGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVASEKEKVWYHVCSSRGKGCYNTRLKEDGGCTI
HGVPYV.NVTLPDEKQNYVH.IGRVGRAERMGLAISLVASEKEKVWY.VCSSRGK..YNTRLKEDGGCTI
RetrocopyHGVPYVTNVTLPDEKQNYVH*IGRVGRAERMGLAISLVASEKEKVWYPVCSSRGKEYYNTRLKEDGGCTI
ParentalWYNEMQ-LLSEIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGNYKGHVDILAPTVQELAALEK
WYNEMQ.LLSE..EHLN.TISQVEPDIKVPVDEFDGKVTYGQKRAAGGG.YK.HVDIL.PT.QEL..LEK
RetrocopyWYNEMQ>LLSE-KEHLNYTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGIYKCHVDILTPTIQELVSLEK
ParentalEAQTSFLHLGYLPNQ
EAQT..L.L..L..Q
RetrocopyEAQTRRL*LNRLRRQ

                            

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

                        

RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_2862 was not experimentally validated.

Retrocopy orthology:

Otolemur garnettii 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008254	1 retrocopy	retro_meug_555,
Myotis lucifugus	ENSMLUG00000003027	1 retrocopy	retro_mluc_1223,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Otolemur garnettii	ENSOGAG00000008730	1 retrocopy	retro_ogar_2862 ,

	RetrogeneDB ID:	retro_ogar_2862
Retrocopy location	Organism:	*Bushbaby (Otolemur garnettii)*
	Coordinates:	GL873672.1:4604046..4605333(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	DDX1
	Ensembl ID:	ENSOGAG00000008730
	Aliases:	None
	Description:	DEAD (Asp-Glu-Ala-Asp) box helicase 1 [Source:HGNC Symbol;Acc:2734]

Parental	LNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEA
	LNNIKQFKKYID.PKLRELLIIGGVAA.DQLSVLENGVDIVVGTPGR.DDL.STGKLNLSQVRFLVL.EA
Retrocopy	LNNIKQFKKYIDSPKLRELLIIGGVAAQDQLSVLENGVDIVVGTPGRMDDLMSTGKLNLSQVRFLVLQEA

Parental	DGLLSQGYSDFINRMHNQIPQITSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVH
	DGLLSQG.SDFINRMHNQIPQITSDGKRLQVIVCS.TLHSF.VKKLSEKIMHFP..VDLK.EDSVPDTVH
Retrocopy	DGLLSQGSDFINRMHNQIPQITSDGKRLQVIVCSVTLHSFNVKKLSEKIMHFPMVDLK-EDSVPDTVH

Parental	HVVVPVNPKTDRLWERLGKNHIRTDDVHA-KDNTRPGANSPEMWSEAVKILKGEYTVRAIKEHKMDQAII
	.VVVPVNPKTDRLWERLG.NHIRT.DVHA.KDNTRP.ANS.EM..EAVKILKG.....AIKEHK.DQ.II
Retrocopy	QVVVPVNPKTDRLWERLGMNHIRTGDVHA<KDNTRPDANSLEM*YEAVKILKGGVYCLAIKEHKKDQTII

Parental	FCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDI
	F.RTKIDCDNLEQYF.QQGGGPDKKGHQF.CV.LHGDRK.HERK.NLERFKKGDVRF..CTDVAA.GIDI
Retrocopy	FYRTKIDCDNLEQYFVQQGGGPDKKGHQFLCVYLHGDRKCHERKKNLERFKKGDVRF--CTDVAASGIDI

Parental	HGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVASEKEKVWYHVCSSRGKGCYNTRLKEDGGCTI
	HGVPYV.NVTLPDEKQNYVH.IGRVGRAERMGLAISLVASEKEKVWY.VCSSRGK..YNTRLKEDGGCTI
Retrocopy	HGVPYVTNVTLPDEKQNYVH*IGRVGRAERMGLAISLVASEKEKVWYPVCSSRGKEYYNTRLKEDGGCTI

Parental	WYNEMQ-LLSEIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGNYKGHVDILAPTVQELAALEK
	WYNEMQ.LLSE..EHLN.TISQVEPDIKVPVDEFDGKVTYGQKRAAGGG.YK.HVDIL.PT.QEL..LEK
Retrocopy	WYNEMQ>LLSE-KEHLNYTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGIYKCHVDILTPTIQELVSLEK

Parental	EAQTSFLHLGYLPNQ
	EAQT..L.L..L..Q
Retrocopy	EAQTRRL*LNRLRRQ

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

RetrogeneDB ID:

retro_ogar_2862