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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 13
gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT
                | | |||   |||   |||  ||  |     |||| |  | |   |   |     |  ||   ||    |  | || | ||    |||||| ||  | || ||  | || ||||||||||||||||||||  | || ||||| |||||||| || || || ||||||||||| |||||||||||||| |
---------------gtctgttg-cgagtgaaataaattcgt-----aagttagttctttttcagacccccaa-aacttaatgttctgttccttattgc--acagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATATGACACACGGAACATCTTCCAGTCACTCGATCTTGCATGGACAT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G181151_T04 (Zea mays), 3'ss of exon 5
--------------------gtctctaataact--ttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT
                     |  ||||   ||  |||    |   |    ||   |           | |    | ||    || |  ||     ||   ||    |  |  | | ||  |  ||||| ||  | || ||  | || ||||||||||||||||||||  | || ||||| || ||||| || || || ||||||||||| |||||||||||||| |
gtctgtttcgagtgaaataaattcctaagggcttgttcgggttgcgtgcagacgtaaccgaacaagccctaagttagttctttttcagatgtccaaaacctaatgttctgttacttcttgct--cagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATACGACACACGGAACATCTTCCAGTCACTAGATCTTGCATGGACAT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT
                      |          | | || || |  ||    ||||       |   |  | ||  |   |||     |  | |  |   ||||||| ||||| || || ||||| ||||| |||||||||||||| || |||||||| ||||| ||||| || || ||||||||||| || || ||||||||| 
----------------------gtctctcttcttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatc-tgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 14
gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggt--actaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT
        ||  | ||  |||| |||| |    |||  | |    | || ||||       |  |||      |||||  |     ||   ||     |   ||||||| |||||||||||  | || || || ||||| || ||||| || ||||||||||||||||||||||| || |||||||| |||||||| ||||||||  
-------gtacatctcactctt-ataaat----tatcatttcatctgaaatgaatccctattgtaagaaaacaactaacaggttgtccgacccttcactggaaacagCTATATCTGGAATTCCTAGACAAATTCGAGAGAAAATTTGTGGCTCAGGGAGCCTATGACACCCGCAACATCTTCCAGTCCCTTGATCTGGCATGGACGC

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|120495604|gb|EH223771.1|EH223771
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|21256304|gb|BQ453192.1|BQ453192
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|11274373|gb|BF324726.1|BF324726
EST:     GGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: GGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|16276744|gb|BI942021.1|BI942021
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|37996030|gb|CF807619.1|CF807619
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAA
EST: gi|7925576|gb|AW831602.1|AW831602
EST:     GAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: GAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|15001046|gb|BI321860.1|BI321860
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|193321576|gb|FK286608.1|FK286608
EST:     TGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: TGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|21601974|gb|BQ612305.1|BQ612305
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|12688253|gb|BG154589.1|BG154589
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
EST: gi|19269615|gb|BM885871.1|BM885871
EST:     AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA
genomic: AGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctaata ... ttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT
                    tactaat  putative branch site (score: 1)
                               ctccccctcccctttt  putative PPT
                                           ttttattaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctaataactttctatcttgataagtactatattttgtttcttcaagtgaaatttcccttgaagtggtactaatggaactccccctccccttttattaacagCTGTATCTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAGGGAGCCTATGACACCCGCAATATATTCCAGTCACTTGATCTTGCATGGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA