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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtag-ctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                           | | |  | ||  ||     |   ||     |    || |  | |  || ||  ||       | |   |||  ||  ||  |  |||| |  || || || || |||||  ||||||| ||||| ||||| || ||||| ||  |||| ||||| |||||||||||||| || |||||||| 
--------------------------gtaagtcttgtt--tgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcact--gcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagt-----tatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                                     || |  |  |  ||  |   | | |   ||    | |     |||||  ||    || ||| ||     |||  |||   ||| || ||||| ||||| |||||| | ||||| ||||| ||||| || ||||| || || |||||||| ||  ||||||| ||||||||||| |||
------------------------------------gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------------------gtattattt-taccgttgtgatattttattaatgatattactgtacaaagagaaaggggggggg------ggggggggtgattagaatgcagttt---gatgtagctgagttatgcttt-tggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                                     | |  |  |||   | |  ||     ||| | || | | |  ||| | |  | || ||  |       |     ||   ||   ||  |||||   |||    ||  | |||| | | | |||| |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  |||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                        | |||  || | |||||| | | |  | ||    |   |  | || |  |||  | |   |   ||||   ||||   || || || ||||||||||||| || ||||||||||| ||||| || || ||||| ||||||||||||||||||||||| ||  | ||||| ||||| || | ||||
-----------------------gtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttg--ggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG

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|208332645|gb|GE129050.1|GE129050
EST:     TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAG                         CAATCGGATTCCAGAGGCT
genomic: TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattatttt ... cttttggcagCAATCGGATTCCAGAGGCT
EST: gi|298182438|gb|HO026613.1|HO026613
EST:     TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAG                         CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA
genomic: TTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattatttt ... cttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
                        gtttgat  putative branch site (score: 5)
                                           tgctttt  putative PPT
             attagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA