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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG

Basic information

species Glycine max
transcript GLYMA08G11130.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG
                                                                                            ||   |  |||| |   ||   |  ||| ||  |   || || |  ||   ||  |   |     |||| |  | ||||| |||||||| ||||| |||||||||||||| ||  |||| ||||| | ||| ||||| |||||||||||||||||| ||||  |
------------------------------------------------------------------------------------------gtaagccccttgttct---atttttgttgcttgtttgg-ataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG

upper sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G044317_T02 (Zea mays), 3'ss of exon 15
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattt----tgatggatgttac---agGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG
                                                                                                           ||| |  |  | ||||  ||   |||     | | ||||||| || ||    | |   ||| | |   |||| |||||||| ||||| ||||||||||| |||||  |||| ||||| | ||||||||| ||||| || || | |||| ||||  |
-----------------------------------------------------------------------------------------------------------gtaagtctcctccatgtgtaacttgaaattgtgccacaagtattacttactctcacacatgctgctccagGATTACACTCCATATTCATGTCAAAAGATCATTTCTGCAACACCTGGCGTTGGAGATCACCATGGATGTCCGTTTCGACATTTTGG

upper sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G044317_T03 (Zea mays), 3'ss of exon 15
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattt----tgatggatgttac---agGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG--------------
                                                                                                           ||| |  |  | ||||  ||   |||     | | ||||||| || ||    | |   ||| | |   |||| |||||||| ||||| ||||||||||| |||||  |||| ||||| | ||||||||| ||||| || || | |||| ||||  |              
-----------------------------------------------------------------------------------------------------------gtaagtctcctccatgtgtaacttgaaattgtgccacaagtattacttactctcacacatgctgctccagGATTACACTCCATATTCATGTCAAAAGATCATTTCTGCAACACCTGGCGTTGGAGATCACCATGGATGTCCGTTTCGACATTTTGGGTACAATTTGACCC

upper sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G67320.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG
                                                 |  ||  || | |    |||  |  | |   |||      || | ||   ||  | || | |   | ||  |        ||||| || |||    |  || |||   || |   || ||||| || || || ||| |||||  |||||| ||  ||||  ||||||| ||||| |||||||| || |||||||||||| |||||||
------------------------------------------------gtaagtacctaactgtcctttctaggccatttttt----tccagagttctcat-ctcttatttatgtcattgaaagtggcaatgatcagcttctgataccaa-attcacattgcaatttcagGATTATACCCCTTATGCTTGTTCAAAGATCATCACATCTGCTCCTGGTGCTGGGGATCATCACGGCTGCCCTTATCGACATTTCAG

upper sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv05s0051g00930.t01 (Vitis vinifera), 3'ss of exon 15
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG
                                                        || |  | | |  | ||   | |   | ||| | || || | |   ||  | ||||     |||||| | |  |  |  |  ||||  ||  | | || |  |     || ||||| ||||| || |||||||||||||| |||||||||||||||||||| |  || |||||||| ||||||||||||||| |||| ||
--------------------------------------------------------ctcacctttttacttaa---aagtgcttaaaaataagatatgac--ttcctatatg-----tgcatgtaaacca--acaacattca--aaacatttttgttttttcctttgcagGATTACACACCTTATTCTTGTCAAAAAATTATTTCATCAACTCCTGGTGTAGGCGATCATCACGGTTGCCCTTATCGACATTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG
                                     ttttgat  putative branch site (score: 4)
                          aacaagtaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA