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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatacatttccctatatttcttcatccctgtaatgactaatgagaagaaacaggagtattttaaagattcttttgatttttttgttgacctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGCGATGATCGCTACTTGGCTGAGCCAGCACTGGACACCGTG

Basic information

species Glycine max
transcript GLYMA05G30140.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30140.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 5
atcatacatttccctatatttcttcatccctgtaatgactaatgagaagaaacaggagtattttaaagattcttttgatttttttgttgacctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGCGATGATCGCTACTTGGCTGAGCCAGCACTGGACACCGTG
|    |  |  | | ||   |  | |       |||    |   |  ||    |  | |   | ||   ||  |||    |   | | |   | |||||||||||| || || ||||| |||||||| || || |||||||||||  | ||||||||||| |||||  ||||| |   |||||| ||| | || || |||
agggaagttacctcaattgcttatgacatgaaaaatattcatctaatagtcttatcaatcagtcaagactttatttatggtagatctggctttatgacagAAAATATGGTCTCGATGACAACACTATTGATTTTATTGGTCATGCAATAGCGCTTCATAGAGATGACTGCTACCTAAATGAGCCTGCAATTGATACTGTG
















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|192322711|gb|FK014402.1|FK014402
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGACAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|193622227|gb|FK569603.1|FK569603
EST:     CTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: CTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|192313375|gb|FK005147.1|FK005147
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|213598704|gb|DB964270.1|DB964270
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|193327075|gb|FK292368.1|FK292368
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208259467|gb|GE053911.1|GE053911
EST:     AAAGAGTTGATAGC                         AAAATACGGTCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: AAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|192313374|gb|FK005146.1|FK005146
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|207755010|gb|GD727407.1|GD727407
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208315534|gb|GE114296.1|GE114296
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208127908|gb|GD922140.1|GD922140
EST:     GGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGTCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: GGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208182690|gb|GD980516.1|GD980516
EST:     ACCCACGAGGGGATGGACTTGGCAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|19347279|gb|BM892159.1|BM892159
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|6915949|gb|AW397479.1|AW397479
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|193497014|gb|FK459492.1|FK459492
EST:     ATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|7924853|gb|AW830879.1|AW830879
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|120533574|gb|EH261707.1|EH261707
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208056662|gb|GD850351.1|GD850351
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|254342789|gb|GR858951.1|GR858951
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
EST: gi|208154706|gb|GD955759.1|GD955759
EST:     ACCCACGAGGGGATGGACTTGACAAGAGTGTCTACTAAAGAGTTGATAGC                         AAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC
genomic: ACCCACGAGGGGATGGACTTGACAAGAGTGACTACTAAAGAGTTGATAGCgtatgtgtgc ... cctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaacaggagtattttaaagattcttttgatttttttgttgacctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGCGATGATCGCTACTTGGCTGAGCCAGCACTGGACACCGTG
                                       tgttgac  putative branch site (score: 3)
             tattttaaagattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatacatttccctatatttcttcatccctgtaatgactaatgagaagaaacaggagtattttaaagattcttttgatttttttgttgacctgtgacagAAAATACGGCCTTGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGCGATGATCGCTACTTGGCTGAGCCAGCACTGGACACCGTG

- catacat
- - - - - - - - - - - -tcatccc
- - - - - - - - - - - - - - - - - - - - - - -gaagaaac