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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatctgttattcaatgtttgttctactagaaaatagttttttgtatccttaattatagactctttctatttataatgcacaaagtgtctatcaggatttcgttttgctttgatttcccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA

Basic information

species Glycine max
transcript GLYMA17G11790.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G34850.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttatctgttattcaatgtttgttctactagaaaatagttttttgtatccttaattatagactctttctatttataatgcacaaagtgtctatcaggatttcgttttgctttgattt-cccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA
                                  |  | ||||||  | ||     || | |      ||   ||| ||     |   ||| | ||  |   ||||  |  |  ||  ||  |   |   | |   | |||| ||  |  || | |||  || | ||   |||| ||| ||| |||| || || || || ||  | |||||  | || ||||| ||  | |||||||| ||| |||| |||||| ||||||||||||||||||||||
----------------------------------gttagtagtttgatctaaatgcaactgtg---ctttaagattcattgcagaggtagtttgtagtattgtttcaatgagagttacttgacttgtttctctagctctgta-ctagccaaactcagtt-ttacttacgaattgtagGCGATATGGGTCAGACATTCAACTCGTTATCCACGTTGGAACATTACATGGAGAGTGGAGCTCAGGCTGTTTTATTTCTTGGAGATCTTTCTTATGCTGA

upper sequence: GLYMA17G11790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0118g00240.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttatctgttattcaatgtttgttctactagaaaatagttttttgtatccttaattatagactctttctatttataatgcacaaagtgtctatcaggatttcgttttgctttgatttcccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA
                                                                            |   ||          | | |  ||| |    | | |||         ||  | |  |||   |   | ||  ||||||    ||   |  || || ||||||||||||| ||||| | ||| || |||||||| ||||||||||| || || |||| ||  ||||||||||||||| | ||||||||||||||||||||
----------------------------------------------------------------------------tgctatcttggtgacttttttttggactcttatctacttgttcggttaatattgtcaattgaatgattgtcgtaaatgaactgttatttgtatgtttcagGTGATTTGGGACAAACATATAACTCCCTTTCCACTCTTGAGCATTACATGCACAGTGAAGGACAGACTGTCTTATTTTTAGGAGATCTTTCTTATGCTGA

upper sequence: GLYMA17G11790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g06520.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttatctgttattcaatgtttgttctactagaaaatagttttttgtatccttaattatagactctttctatttataatgcacaaagtgtctatcaggatttcgttttgctttgatttcccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA
                                                         ||   ||  | | | | || ||     |   | | | ||| ||         ||| ||  || | |  |   ||| | ||   |  ||| |          ||||  |  | |||  |||||||||||| ||||| | |||||||||||| || || |||||||| || || |||||||| ||||||||||||||||| || ||||| |||||||||||
-------------------------------------------------------cgataccagg-tttctttcttcatgtgcaattgaatttttataag---------ttgattacatattctctagatttaaattctcatttctta----------attg-gtttacattttagGTGATTTGGGTCAAACATATAATTCTCTTTCTACACTCGAGCATTACATGCAGAGTGGAGCACAGACTGTCTTATTTGTCGGTGATCTCTCTTATGCTGA

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|193432592|gb|FK394278.1|FK394278
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGG
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGG
EST: gi|193689287|gb|FK632660.1|FK632660
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|193718891|gb|FK654821.1|FK654821
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGG
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGG
EST: gi|207680921|gb|GD662816.1|GD662816
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGG
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGG
EST: gi|254324086|gb|GR840511.1|GR840511
EST:     TCCCTACAAATTTGGGATCATTG                         GTGATTTGTGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: TCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|151407026|gb|EV276841.1|EV276841
EST:     ACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: ACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGG-ATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|193593904|gb|FK546146.1|FK546146
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|207802621|gb|GD773904.1|GD773904
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|208173897|gb|GD966808.1|GD966808
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|208165423|gb|GD961591.1|GD961591
EST:     AACACCTCCCAAGGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGG
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGG
EST: gi|23726031|gb|BU760993.1|BU760993
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|254344611|gb|GR855482.1|GR855482
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|192299966|gb|FG991812.1|FG991812
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|208111807|gb|GD913305.1|GD913305
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|193563452|gb|FK521341.1|FK521341
EST:     TCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: TCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|6727109|gb|AW311463.1|AW311463
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|193492541|gb|FK457457.1|FK457457
EST:     TCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: TCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|120530447|gb|EH258580.1|EH258580
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCCTTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCT
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCT
EST: gi|193461361|gb|FK428074.1|FK428074
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         -TGATTTGGGG
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGG
EST: gi|254343421|gb|GR857125.1|GR857125
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|209728180|gb|BW651615.1|BW651615
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|192311725|gb|FK003586.1|FK003586
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|19453471|gb|BM954881.1|BM954881
EST:     AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: AACACCTCCCAAAGTTGATCCAGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
EST: gi|193702858|gb|FK639206.1|FK639206
EST:     TCCCAAAGTTGTATTCCTAGATTCTCCCTACAAATTTGGGATCATTG                         GTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC
genomic: TCCCAAAGTTG-A-TCC-AGATTCTCCCTACAAATTTGGGATCATTGgtaagttatc ... aatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA
                     ctctcac  putative branch site (score: 3)
      atttttattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatctgttattcaatgtttgttctactagaaaatagttttttgtatccttaattatagactctttctatttataatgcacaaagtgtctatcaggatttcgttttgctttgatttcccatgatttttattttgtagctctcacaaatgagtcattgcataaatattgcagGTGATTTGGGGCAAACGTTTAATTCTCTTTCCACCCTTGAGCATTATATACAAAGTGGAGCGCAGACTGTCTTATTTGTTGGAGATCTTTCTTATGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG