RetrogeneDB ID:

retro_chof_1503

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_310343:113..864(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:STX7
Ensembl ID:ENSCHOG00000010117
Aliases:None
Description:syntaxin 7 [Source:HGNC Symbol;Acc:11442]


Retrocopy-Parental alignment summary:






>retro_chof_1503
GGAATTGGTGGGGACCCTGCCCAATTGGCCCAGAACATCTCTTCCAACACCAAGAAGATCACACAATGTTCTGTGGAAAT
ACAAAAGCCTCTGAATCAACTTGGAGCACCCCAAGATTCTCCCAAATTGAGGCAACAGCTGCAACAGAAACAGCAGTATA
CTAACCATCTTGCCAATGAAACAAATAAACACATTAAAGAGTTTGGATTTCTTCTCACCACCCTCCAATGAACAGCAGCA
AAAGAAAATAAAGAAGGATTGCTTAGTGGCTGAATTCACAACCTCACTGACAAACTTTCAGAAGGTCCAGAGGCAAGTTG
CTGAGGGAAAAAGGAGTTTGTTGTTGAAGCAAGAGTCAGCTCCAAGGTATCTGGTGGTTTTCCAGATGAAGGGAATCTTG
TATCCTGGGAAAGCCAAACTCAACCTCAAGTGCATGTGCAGGATGAAGATATTACAGAGGATGACCTCTGCTTCATTCAT
GAGGCAGAGTCTTCTACTAGACAACACAAAGCTGATTATTATGGATATTAATGAAATATTTAAAGATTTAGGAATGATGA
TTTAAGAACAAGGAGATGTCACAGATAGCATAGAAGTCAATGTAGAAAATGCTGAGGTGCACATTCAACAAGGAAACCCG
CAGCTGTCAAGGGCAGCAGATTACCGGTGCAAATCCAGAAAAACTCTGTTCACCATCATTTTTATCCTTGTCATTGGATT
TGTGATTACTGGTCTCATCATATGGGGAGTG

ORF - retro_chof_1503 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.37 %
Parental protein coverage: 97.31 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGIGGDPAQLAQRISSNIQKITQCSMEIQRTLNQLGTPQDSPELRQQLQQKQQYTNQLAKETDKLIKEFGS
GIGGDPAQLAQ.ISSN..KITQCS.EIQ..LNQLG.PQDSP.LRQQLQQKQQYTN.LA.ET.K.IKEFG.
RetrocopyGIGGDPAQLAQNISSNTKKITQCSVEIQKPLNQLGAPQDSPKLRQQLQQKQQYTNHLANETNKHIKEFGF
ParentalLPTT-PSEQRQRKIQKDRLVAEFTTSLTNFQKVQRQAAE-REKEFVARVRASSRVSGGFPEDTSKERNLV
L.TT...EQ.Q.KI.KD.LVAEFTTSLTNFQKVQRQ.AE...KEFV...R.SS.VSGGFP........LV
RetrocopyLLTT>SNEQQQKKIKKDCLVAEFTTSLTNFQKVQRQVAE<GKKEFVVEARVSSKVSGGFPDEGN----LV
ParentalSWESQTQPQVQVQDEEIMEDDLRLIQERESSIRQLEAD-IMDINEIFKDLGMMIHEQGEVIDSIEANTEN
SWESQTQPQV.VQDE.I.EDDL..I.E.ESS.RQ..AD.IMDINEIFKDLGMMI.EQG.V.DSIE.N.EN
RetrocopySWESQTQPQVHVQDEDITEDDLCFIHEAESSTRQHKAD>IMDINEIFKDLGMMI*EQGDVTDSIEVNVEN
ParentalAEMHVQPANQQLSRAAGYQRKSRKTLCIIIFSLGTG-VIISFIIWGV
AE.H.Q..N.QLSRAA.Y..KSRKTL..IIF.L..G.VI...IIWGV
RetrocopyAEVHIQQGNPQLSRAADYRCKSRKTLFTIIFILVIGFVITGLIIWGV

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1503 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni 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 8 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000010117 3 retrocopies
retro_chof_1503 , retro_chof_2631, retro_chof_829,
Dasypus novemcinctus ENSDNOG000000002951 retrocopy
Felis catus ENSFCAG000000022921 retrocopy
Myotis lucifugus ENSMLUG000000043011 retrocopy
Sarcophilus harrisii ENSSHAG000000144401 retrocopy
Tursiops truncatus ENSTTRG000000098531 retrocopy



Copyright © RetrogeneDB 2014-2017