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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctttctgcatctttcttctctttcatgtgcacgagggtactaattaatgggtaattatgtgatagtaattgagtgatgattgtaactatttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG

Basic information

species Glycine max
transcript GLYMA07G09180.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 6
cctttctgcatctttcttctctttcatgtgcacgagggtactaattaatgggtaattatgt-gatagtaattgagtgatgattgtaa-ctatttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
 || |||   |||  | | | ||  |  |||| | |||||   ||    || |   ||||  |    |||||||   |||||| |||  | ||| ||| ||||||||||| |||| || ||||||||| ||||||||||| || |||
-ctctctctctctcccct-tgttcaacatgcatgtgggtatgtataggaggatgtgtatgaaggccttaattgatcaatgattataaattttttcatgttagGTTCAAGGGGAGAGGAATTGTATATTTCCTGAAGACCCTGGCCAG
















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|13312217|gb|BG405798.1|BG405798
EST:     GGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGAGTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|120493761|gb|EH221928.1|EH221928
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|120493651|gb|EH221818.1|EH221818
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|7685006|gb|AW755654.1|AW755654
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|19348059|gb|BM892591.1|BM892591
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|192312979|gb|FK004625.1|FK004625
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|4287805|gb|AI441242.1|AI441242
EST:     CTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: CTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|208239088|gb|GE037166.1|GE037166
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGAGTTGTATATT
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATT
EST: gi|23053843|gb|BU577597.1|BU577597
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|192312980|gb|FK004626.1|FK004626
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|31463138|gb|CD405166.1|CD405166
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGAGATGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|21677113|gb|BQ629464.1|BQ629464
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         GTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
EST: gi|19348345|gb|BM892877.1|BM892877
EST:     GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCT                         G---A-G-AGA-A-GACTTGTATATTCCCTGAAGACCCCGGTCAG
genomic: GCTTACCATACTTGAGCGGTGGATCAGGGAACACGAGGCAGCAACATTCTgtaagaaata ... ttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgggtaattatgtgatagtaattgagtgatgattgtaactatttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG
                                  attgtaactatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctttctgcatctttcttctctttcatgtgcacgagggtactaattaatgggtaattatgtgatagtaattgagtgatgattgtaactatttaatgctagGTTCAAGGAGAGAAGACTTGTATATTCCCTGAAGACCCCGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - -ctgcatc
- - - - - - - - - - - - - - tgcacga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga