RetrogeneDB - Retrocopy retro_tsyr

                        
>retro_tsyr_27
ATGACAGATGCCCCTGTGTCCTTCGCCAAGGACTTCCTGGCAGGTGGAGTGGCCGTGGCCATCTCCAAGACTGCGGTAGC

GCCCATCGAGCGGGTCAAGCTGCTGCTGCAGGTGCAGCATGCCAGCAAACAAATCACTGCAGATAAGCAATACAAGGGCA

TTATAGACTGTGTGGTCCATATCCCCAAGGAGCAGGGAGTCCTGTCCTTCTGGCGTGGTAACCTGGCTAATGTCATCAGA

TACTTCCCCACCCAGGCGCTCAACTTTGCCTTCAAAGATAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAGAGGAC

CCAGTTTTGGCGCTACTTTGCAGGGAATCTGGCGTCAGGCGGTGCCGCTGGGGCCACATCCTTGTGTTTTGTGTACCCTC

TTGATTTTGCCCGTACCTGTCTAGCAACTGATGTGGGTAAAGCCGGAGCTGAAAGGGAATTCAGAGGCCTCCGTGACTGC

CTGGTTAAGATCTACAAATCTGATGGGATTAAGGGCCTGTACCAAGGCTTTAACGTGTCTGTGCAGGGTATTATCATCTA

CCGAACTGCCTACTTCGGTATCTATGATACTGCAAAAGGAATGCTTCCAGATCCCAAGAATACTCACATCATCATCAGCT

GGATGATTGCACAGTCTGTCACTGCTGTTGCTGGGTTGACTTCCTATCCATTTGACACTGTCCGTCGCCGCATGATAATG

CAGTCAGGGCGCAAAGGAACTGATATCACGTACACAGGCACACTTGACTGCTGGAGGAAGATTGCTCATGACGAAGGAGG

CAAAGCTTTTTTCAAGGGTGCATGGTCCAACGTTCTCAGAGGCATGGGTGGTGCTTTTGTGCTTGTCTTGTACGATGAAA

TCAAGAAGTACACATAA

ORF - retro_tsyr_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.08 %
Parental protein coverage:	99.62 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHK
VQHASKQI.A.KQYKGIIDCVV.IPKEQG.LSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVD...
RetrocopyVQHASKQITADKQYKGIIDCVVHIPKEQGVLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRT
ParentalQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFSGLGNCITKIFKSDGLKGLYQGF
QFWRYFAGNLASGGAAGATSLCFVYPLDFART.LA.DVGK..A.REF.GL..C..KI.KSDG.KGLYQGF
RetrocopyQFWRYFAGNLASGGAAGATSLCFVYPLDFARTCLATDVGKAGAEREFRGLRDCLVKIYKSDGIKGLYQGF
ParentalSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIAQSVTAVAGLVSYPFDTVRRRMMMQSGRKGA
.VSVQGIIIYR.AYFG.YDTAKGMLPDPKN.HI..SWMIAQSVTAVAGL.SYPFDTVRRRM.MQSGRKG.
RetrocopyNVSVQGIIIYRTAYFGIYDTAKGMLPDPKNTHIIISWMIAQSVTAVAGLTSYPFDTVRRRMIMQSGRKGT
ParentalDIMYTGTVDCWRKIAKDEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY
DI.YTGT.DCWRKIA.DEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY
RetrocopyDITYTGTLDCWRKIAHDEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY

                            

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

                        

RNA-Seq - click to see more details

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tarsius syrichta was not studied using ChIP-Seq data.

EST - click to see more details

Tarsius syrichta was not studied using EST data.

TSS - click to see more details

Tarsius syrichta was not studied using FANTOM5 data.

Lab - click to see more details

retro_tsyr_27 was not experimentally validated.

Retrocopy orthology:

Tarsius syrichta 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 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27 ,

	RetrogeneDB ID:	retro_tsyr_27
Retrocopy location	Organism:	*Tarsier (Tarsius syrichta)*
	Coordinates:	scaffold_264945:2552..3449(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSTSYG00000014778
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	SLC25A4
	Ensembl ID:	ENSTSYG00000004233
	Aliases:	None
	Description:	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Parental	VQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHK
	VQHASKQI.A.KQYKGIIDCVV.IPKEQG.LSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVD...
Retrocopy	VQHASKQITADKQYKGIIDCVVHIPKEQGVLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRT

Parental	QFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFSGLGNCITKIFKSDGLKGLYQGF
	QFWRYFAGNLASGGAAGATSLCFVYPLDFART.LA.DVGK..A.REF.GL..C..KI.KSDG.KGLYQGF
Retrocopy	QFWRYFAGNLASGGAAGATSLCFVYPLDFARTCLATDVGKAGAEREFRGLRDCLVKIYKSDGIKGLYQGF

Parental	SVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIAQSVTAVAGLVSYPFDTVRRRMMMQSGRKGA
	.VSVQGIIIYR.AYFG.YDTAKGMLPDPKN.HI..SWMIAQSVTAVAGL.SYPFDTVRRRM.MQSGRKG.
Retrocopy	NVSVQGIIIYRTAYFGIYDTAKGMLPDPKNTHIIISWMIAQSVTAVAGLTSYPFDTVRRRMIMQSGRKGT

Parental	DIMYTGTVDCWRKIAKDEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY
	DI.YTGT.DCWRKIA.DEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY
Retrocopy	DITYTGTLDCWRKIAHDEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKKY

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

RetrogeneDB ID:

retro_tsyr_27