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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaacactttaatacaagttttatgatattattacaatagttgtacatggacttgggaactgtttttgttagattatttgcattttatatttttgtattgttgtctgatcatcacttgtttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCTGGACGCTGCTTTAATTGTGGCCTTGATGGTCATTGGGCACGGGATTGCA

Basic information

species Glycine max
transcript GLYMA03G33260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33260.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 2
gtatgaaacactttaatacaagttttatgatat-tattacaatagttgtacatggacttgggaactgtttttgttagattatttgcattttatatttttgtattgttgtctgatcatcacttgtttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCTGGACGCTGCTTTAATTGTGGCCTTGATGGTCATTGGGCACGGGATTGCA
              | ||  |  | |||| ||| || | |  |     || ||||  |||  |    |||||  |  | ||| | | ||  ||  |  | |  ||| |   |       |  ||  |  ||||||       ||| || || |||||| | || ||||||||||| ||||| |||||||||||||| ||||||||| ||||||| || ||||            
--------------attattatgtgtatggtatctagttctctgacaata-atggttttgtcatacatttttaatttaatatattctttcaatggtgctttgatgtgggtggtagGGACCCCGTGGTGGATCAGG-------TGGTTCTCGAGAATATCTAGGTCGAGGTCCTCCGCCTGGGTCTGGACGCTGCTTCAATTGTGGCATTGATGGCCACTGGG------------
















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|192319241|gb|FK006941.1|FK006941
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|298189291|gb|HO037694.1|HO037694
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|192319242|gb|FK006942.1|FK006942
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|298170069|gb|HO018693.1|HO018693
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|208324972|gb|GE124870.1|GE124870
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|213589600|gb|DB965816.1|DB965816
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|151403736|gb|EV273546.1|EV273546
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|192324223|gb|FK017954.1|FK017954
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|213597756|gb|DB960313.1|DB960313
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|298193736|gb|HO040384.1|HO040384
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|193382544|gb|FK345797.1|FK345797
EST:     GGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: GGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
EST: gi|192334590|gb|FK025179.1|FK025179
EST:     ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGG                         GCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT
genomic: ATGGTCGGGATGTTGATGGAAGTCGTATTATTGTGGAATTTGCAAAAGGGgtatgaaaca ... ttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgcattttatatttttgtattgttgtctgatcatcacttgtttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCTGGACGCTGCTTTAATTGTGGCCTTGATGGTCATTGGGCACGGGATTGCA
                            gtctgat  putative branch site (score: 4)
                                        cttgttttt  putative PPT
       attttatatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaacactttaatacaagttttatgatattattacaatagttgtacatggacttgggaactgtttttgttagattatttgcattttatatttttgtattgttgtctgatcatcacttgtttttaatcagGCTCCTCGTGGGTCCCGGGAATATTTGGGGCGAGGTCCTCCTCCTGGCTCTGGACGCTGCTTTAATTGTGGCCTTGATGGTCATTGGGCACGGGATTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT