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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgattcttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT

Basic information

species Glycine max
transcript GLYMA20G35900.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgattcttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT
                                    | | || | |  ||    |  |||||    ||   |   | |  ||| | |   | | |||  |   ||| |  || | ||   | |||  |||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||| ||||| |  |  ||  | || | |     |||   |
-----------------------------------gtgagttta-atctgcctttctttcttttgcaat--agcattataaagctcatttattaatattaatctgt-taatgctttc--tgatta--acagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT

upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G73390.2 (Arabidopsis thaliana), 3'ss of exon 12
gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgattcttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT
                                | | ||| || | || |  |   || | ||   |        |  | ||  ||          |||  |||    || | ||     ||   |||| || ||||||||||||||||||||  | ||||||||||||||||| |||||||| ||||| || || ||||||   || ||| | || |||     ||  | |
-----------------------------gtgagtttcagtttaaagctt-tgtcgagttttatctcttcttttgctatgatattt---------taagctcaatctttctatttatgccga--attatagGATCATGGAGACAGCACCAACGCTTCCTGATTTTGCCTTGGCATTGAAACCCGATGAGTACCAACTTCCTTCTGTTGATGCGTCATGGTCTGAAGCCAGT

upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv16s0039g00390.t01 (Vitis vinifera), 3'ss of exon 13
gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgatt-cttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgctt-attacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAG-AACAGAAAAT
       | |||   |   |    ||||||    | | | |  ||   || |    ||| || |  | |   || | || |||| || |  |   ||    | ||| ||  |  ||  ||  ||| | | ||||||||||||||||||||||  | ||||||||||||| |||||  ||||||| ||||| || || |||||||  ||||| || |||||||   |||  | | 
------gtaagtctttctttgg--tgttttggcgtttaactctatgcctgttggccattactggaatgaatgaatgaaatgaagctggaaaatc-attctgtgatgagtgatactggaaaatcttgactgcagAATCATGGAGACAGCACCACAACTGCCTGATTTTGCTTTGGCCCTGAAACCCGATGATTACCAACTTCCTCCAGTGGACCCTTCTTGGAACGACAACATA-

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|18038689|gb|BM306983.1|BM306983
EST:     GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
EST: gi|193623310|gb|FK574660.1|FK574660
EST:     GATACTTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
EST: gi|151398827|gb|EV268698.1|EV268698
EST:     GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
EST: gi|151404759|gb|EV274573.1|EV274573
EST:     GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
EST: gi|151394195|gb|EV264066.1|EV264066
EST:     GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
EST: gi|22932509|gb|BU549648.1|BU549648
EST:     GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAG                         AATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC
genomic: GATACCTCAAGCAAGGTGCGAATAAACCGTGATCTGTACTCCTATGAGAGgtaagcatta ... cttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT
             gactgat  putative branch site (score: 3)
                  ataaaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgattcttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA