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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttattttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG

Basic information

species Glycine max
transcript GLYMA02G13160.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g31220.1 (Oryza sativa), 3'ss of exon 6
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttatttttt-ttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                                                                      |||  | |  | ||||     | ||          ||   ||| |  |    | ||   |   ||   ||   |||||| |    |  || ||  |    ||||||  |  |||||||| |||| ||||| ||||| ||||||||  |||||||||||||||| ||  |||| || |||||||||||| ||
--------------------------------------------------------------------gtacctcttacatatttagattgacgatggcattcaaatgtgactctccttgtcatatctcatatatgccct---ttctttgtactaaaaaagtatcttgcaatttttgatgtagGGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTTGATATG

upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g42110.1 (Oryza sativa), 3'ss of exon 10
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttatttttt-ttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                                                                      |||  | |  | ||||     | ||          ||   ||| |  |    | ||   |   ||   ||   |||||| |    |  || ||  |    ||||||  |  |||||||| |||| ||||| ||||| ||||||||  |||||||||||||||| ||  |||| || |||||||| ||| ||
--------------------------------------------------------------------gtacctcttacatatttagattgacgatggcattcaaatgtgactctccttgtcatatctcatatatgccct---ttctttgtactaaaaaagtatcttgcaatttttgatgtagGGAATTATTGTATTGGCTGCTACTAATCGCCCAAATGCAATTGATGCTGCTCTTCTGCGCCCAGGGCGTTTCGATATG

upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G149994_T02 (Zea mays), 3'ss of exon 10
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttatt-ttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG----------------------
                                                                                                  |||  ||  | |||| | |    | |||  ||   || || |     ||   ||  |||| ||||||     ||  |||||| |||||||| | || ||||  ||||| ||||||||  |||||||||||||||| ||  ||||||| |||||||| |||  |                      
------------------------------------------------------------------------------------------gtactgttagcctgctgataactttctgt--gtgattctactgattatat-----ctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAGGTCCTTCAGTGCTTCTGTTAAT

upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G149994_T01 (Zea mays), 3'ss of exon 8
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttatt-ttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                                                                                                  |||  ||  | |||| | |    | |||  ||   || || |     ||   ||  |||| ||||||     ||  |||||| |||||||| | || ||||  ||||| ||||||||  |||||||||||||||| ||  ||||||| |||||||| |||  |
------------------------------------------------------------------------------------------gtactgttagcctgctgataactttctgt--gtgattctactgattatat-----ctacatgtatattcactagaaggcaatcctttttttagGGAATTATCGTATTGGGTGCTACGAATCGCCCAAATGCAATTGATGCTGCTCTTTTGCGTCCAGGGCGTTTCGATAAG

upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G03670.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttattttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                                                                                             | |||   ||||  | |    | || ||||  |  |     | ||   ||| |  |   | |||| |   | | ||  ||     | ||||||| || || ||||| || ||||| ||||| ||||||||||||||||| || ||||| ||||| || |||||||| 
---------------------------------------------------------------------------------------------gtaaacaaaagctcataggctt-ttaaagattttatctttgttattgggttgcaat---gatattgatcgggttttggtt-----taagGGAATCCTCGTCTTGGCTGCCACAAACCGCCCGTATGCAATTGATGCTGCTCTAATGCGACCTGGTCGATTTGATCTC

upper sequence: GLYMA02G13160.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0071g00680.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttattttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                                                              || | || ||   |  ||| ||| ||||   ||     |    |  ||| |  ||                |  ||| |  ||||     | | | |  |    ||     ||||| |||||||||||||||||||| ||||| ||||| ||  ||||||||||||||||||| ||||| ||||| ||||||||||||
--------------------------------------------------------------ttacatctact-gttcattttttgtcaa---gattgttcggataagaaattagatc-------------atacaatccaacttctgc---gatttgagtttttgctcatcctttttacagGGAATTCTTGTTTTGGCTGCTACTAATCGACCTCATGCAATTGATGCTGCACTAATGCGCCCTGGACGTTTTGATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggcatcatctagtttctttctggctattaactagatctttattttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG
                           tattaac  putative branch site (score: 1)
                                      tctttattttttttc  putative PPT
                           tattaactagatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatgcctttttcttctttgatgtttgttttaatgacattttatcctctccctgtccttttcctccacccatgaattctttatcaaaaggaaaaagcaagcataaaactgtattcaagagatggtaggcatcatctagtttctttctggctattaactagatctttattttttttcagGGAATTCTTGTTTTGGCAGCTACAAATCGCCCCTATGCAATTGATGCTGCACTCATGCGTCCTGGGCGTTTTGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC