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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatagaaaactgctcagggtgataggattatttggatgcgcctttaatgttatcagctattgtgagtgtgttaacaagttctgttatttcttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTGCAAAAATAAT

Basic information

species Glycine max
transcript GLYMA13G06410.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 2
gcatagaaaactgctcagggtgataggattatttggatgcgcctttaa------tgttatcagctattgtgagtgtgttaacaagttctgttatttctta-taccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTGCAAAAATAAT
       || | | |  ||  |||    || |    |  |    | ||      ||   |      || |     || || |   ||    ||||| ||| | |||||| | |||| |||||||||| ||||||| |||||||| || ||| |||| | |||||||||||   ||||||| | |||  ||||| |||||||||| | 
-------aagcagttttggtcgatcaagttgtgcaaaaacaaaatcaagtaagatgaagttcctctttatataaatgatatctgatttatatattttttaatcccagATCTTGAGTGCATCTTCACTGTCATCTGTAATCTTGTCACGAAGTCTGAAAGTCCAGATGAAGCATTGGAGATGGCAAAGTTTATATCTGCAAAAATTAC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|209706659|gb|BW667874.1|BW667874
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACCAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
EST: gi|192325549|gb|FK018445.1|FK018445
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
EST: gi|20812919|gb|BQ297397.1|BQ297397
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACCAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
EST: gi|120533886|gb|EH262019.1|EH262019
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
EST: gi|8827888|gb|BE211618.1|BE211618
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
EST: gi|16347357|gb|BI972952.1|BI972952
EST:     ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAG                         ATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA
genomic: ATTGATGATTACCTCTGCTGAATTGGTTTTCTCAAAGGTTTCTGAAACAGgtagaatgct ... cttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgttatcagctattgtgagtgtgttaacaagttctgttatttcttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTGCAAAAATAAT
                        tgttaac  putative branch site (score: 2)
                                  ttctgttatttctt  putative PPT
                                     tgttatttcttata  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatagaaaactgctcagggtgataggattatttggatgcgcctttaatgttatcagctattgtgagtgtgttaacaagttctgttatttcttataccagATATAGAGTCCATCTTCACTATCATCTGCAATCTTGTGACAAAGACTGAGAATCCAGATGAAGTGATGGAGATTGTAAAAGTTATAACTGCAAAAATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - ctgctca
- - - - - - - - - - - - - - - - -tggatgc
- - - - - - - - - - - - - - - - - - - - gccttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtg