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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT

Basic information

species Glycine max
transcript GLYMA13G06840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 3
tgctgctattaacttgttgttggtagtggaaaacacactattag-aagagcaggatctttggagattattct-tactt-ttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
 | || |   ||        ||  |    |        ||  |  | || ||   | | ||   |  ||| | ||||  |||||  | | | | |   |||||| || |||   |||||||| | |||| | |   | ||||| |||||||| |||||||| || ||||||||||||||||| ||||||||    || |||||
-gttgattgaaaaaaaaaactgacatcaaatctgttgttagcaccatgaacaatttatctgcctaagattttgtactaattcttacattatatcta--tgcagATTATACTTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGT

upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G468260_T02 (Zea mays), 3'ss of exon 2
tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttctt------caactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
    |     ||  ||||        ||   |  ||| | ||      |    |  ||   |    ||||| ||| || ||       ||      |   ||||||| ||   |   |||||||| | |||| | |   | ||||| || ||||| |||||||| || ||||||||||||||||| ||||||||    || |||||
----gaacgaaaggtgttcaaaactatgagcattacattttttctgttg--atactttataatcacattctcactattgttatatattaatgtaactaaattgcagATTATGATTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGT

upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
--tgctgctattaact-tgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
  |   || |||||   | | |||      |   |    |   ||   || |||  |   |   | |||  | | |   |||||    | |       |||||| ||||||   |||||||| |||||||| || || || ||||| ||||| |||||| | || |||||||| ||||||||||||||||| |  || || ||
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggt--aatattggtttcatagttctttg-ttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT

upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G02290.1 (Arabidopsis thaliana), 3'ss of exon 3
tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattct-tacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
                         ||   ||  |  | |||  |    |||  || ||   | |  |||  || |  | |     || ||||  |||||||||| ||   |||||| ||||||||  |||||||||| || || ||||| |||||| ||||||||||||||||||||||||||||||| |||||||| ||
-------------------------gtaataataatcccattcaa----cagtctcctttttgttccttcagtattcatatcttgttggtttt--ttgcagAATATACATCAGAGAACCCAAAGATTGTGACAAAATGTTCACACCATTTCCACCTTAGTTGCATTTATGAGTGGATGGAGAGAAGTGAAAACTGTCCAGT

upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G15790.2 (Arabidopsis thaliana), 3'ss of exon 3
tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggaga-ttattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
           | |  || |      |      |    | || ||  |      |     ||   ||| | | |  ||  |||   ||||||     | ||||||||    |||||| || |||||  | ||||| || ||||| ||||| |||||  ||||||||||||| ||||||||||||||||| ||||| |||||
---------gtattcattttcatctttttttttctttttcttggatcaatgcatttcaaagaagcttagtatcagattatttcgtgtgtttt-----gtagAATACATATCAGAGAACCCGAAGATTGTTACAAAGTGTTCTCACCATTTCCACCTCAGTTGCATTTATGAATGGATGGAGAGAAGTGAAAACTGCCCTGT

upper sequence: GLYMA13G06840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0083g01000.t01 (Vitis vinifera), 3'ss of exon 3
-tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
 |  ||  ||||    |||| || |  ||  ||    |||   | |  || |   | || ||  ||   |  |  |||  |   |||  | ||   ||||||||| |||  ||| ||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||| |  ||||| ||
atcttgtcattattaggttgatgattctgttaactgtactcaaatattag-aatgttttagggtatagattctgatttgttcatacttatcttttatgcagAATATACTCCAGAAAATCCCAAGATAATGACAAAATGCTCTCACCATTTTCACCTTGGTTGTATATATGAATGGATGGAGAGAAGTGAAACATGTCCAGT

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|192304212|gb|FG996394.1|FG996394
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|37997745|gb|CF809334.1|CF809334
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|192304187|gb|FG996383.1|FG996383
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|8826638|gb|BE210368.1|BE210368
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|9985548|gb|BE659656.1|BE659656
EST:     CTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: CTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|57575660|gb|CX548635.1|CX548635
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|58015626|gb|CX702368.1|CX702368
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|192304213|gb|FG996395.1|FG996395
EST:     TGTTTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|151395159|gb|EV265030.1|EV265030
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|192300484|gb|FG987911.1|FG987911
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|192299720|gb|FG993300.1|FG993300
EST:     GCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTTTCATCATTTTC
genomic: GCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|58015294|gb|CX702036.1|CX702036
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtagatatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT
                      ttcttac  putative branch site (score: 2)
                                          tttttgctt  putative PPT
                  attattcttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgctattaacttgttgttggtagtggaaaacacactattagaagagcaggatctttggagattattcttacttttcttcaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
tgctgct
- - - - - - cttgttg
- - - - - - - - - - -ggtagtg
- - - - - - - - - - - - - - - -aacacac