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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcctaaacgattgcaactcattggcaagttttttattttatgaaactgattgatttattgattatatgttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCACTACCTTGGTTCGGTTCTTGGTCGCTATGATGGAGATGTGTATCCAAAGC

Basic information

species Glycine max
transcript GLYMA05G04940.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtcctaaacgattgcaactcattggcaagttttttattttatgaaactgattgatttattgattatatgttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCACTACCTTGGTTCGGTTCTTGGTCGCTATGATGGAGATGTGTATCCAAAGC
||||||  |  |   |||        |  | | | | |||| | || | | |  || |||    |   ||   |  | ||||||  ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||| ||| ||||  |||| ||  ||||||||||| ||||||||||||| |
gtttgtttttgaactttgtt-----ctatccattatcttatgtgatcagattactt-attcgaagtccatgattggttgttagGCCCGTCCAAATGCCATTGCCCTTGTTGATGCATTTAACTACACCGATCACTATCTTAGTTCTATTCTCGGCTGCTATGATGGAAATGTGTATCCAAAAC
















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|151404520|gb|EV274334.1|EV274334
EST:     CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|192328166|gb|FK022860.1|FK022860
EST:     CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|193334136|gb|FK300838.1|FK300838
EST:     TTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: TTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|14991267|gb|BI316940.1|BI316940
EST:     CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|192321454|gb|FK011740.1|FK011740
EST:     CCAAACAGG-TTCCCTTGCAA-TGAGCTGCTGAG-TCCT-GTATTCACAG                         -TTCGTCCTAATGCAATTGCACTTGT-GATGCGTTTA-CTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|9204243|gb|BE330467.1|BE330467
EST:     CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
EST: gi|192328167|gb|FK022861.1|FK022861
EST:     CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAG                         GTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC
genomic: CCAAACAGGGTTCCCTTGCAAATGAGCTGCTGAGGTCCTTGTATTCACAGgtttgtccta ... ttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagttttttattttatgaaactgattgatttattgattatatgttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCACTACCTTGGTTCGGTTCTTGGTCGCTATGATGGAGATGTGTATCCAAAGC
                                tattgat  putative branch site (score: 3)
     ttttttattttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcctaaacgattgcaactcattggcaagttttttattttatgaaactgattgatttattgattatatgttttggttagGTTCGTCCTAATGCAATTGCACTTGTTGATGCGTTTAACTACACTGATCACTACCTTGGTTCGGTTCTTGGTCGCTATGATGGAGATGTGTATCCAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG