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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC

Basic information

species Glycine max
transcript GLYMA06G08780.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtg-atgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                     | |  ||||||| |||     ||| |       |||||||  ||   | |  ||| | ||   |  | ||||   |    | | |  | || | |  ||     |||   | |  | |    ||||  ||| | || | || ||||| |||||||| || ||||||||||| |||||||| || |||||||| ||||||||||||||||| |      
-----------------------------------cgagtattttttgg-atgccatgtttca-------tttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaa-----ttgccagGAGGCGGCTG-GTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g17460.1 (Oryza sativa), 3'ss of exon 4
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaata-tcttgtttgaacacagGAATG----TGAA---ATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                                     ||| ||   | |  | ||| || |      | |||   | |   ||  || |  | |||   || |  |    ||  |||| | | |||| | |||      | ||     ||||   || |     |||  |||||||||||| || |||||||||| ||| ||||  ||| | || ||||| ||||| ||||||||||| |      
----------------------------------------------------aatgtttaggaat--aatttgttatttcccca-ttaaaatgccaagtccattttttttttaccttgagctaca-tgtgtttatacagtcttatgtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                    |||    |  ||  || |||   |||  |    |||  | ||     | ||| ||| |||        ||| || |    | | || | || |||  ||     ||| | | |       | ||||  | |   || |||| ||||| |||||||| || || |||||||| ||||| ||||| |||||||| ||||||||||||||||| |      
-----------------------------------ctatcaaatactgaaattatgtcatta--ttgcatttaatttggaccaagttattgtgctgc-----catgacatgtggcattaattctagtccatgaaa-----ttgctagGAGGTGTCTA-GTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                     ||   ||   ||||| ||    |||   ||  |  |||  |   ||  ||| ||| |||  || |   |  |  ||| ||      | || |||    | || |||   | |       | ||||  | |   || |||| ||||| |||||||| || || |||||||| ||||| || || |||||||| ||||||||||||||||| |      
-------------------------------------atcaattacaggcattatatcattattgcatttcattt-cggccatg-ttattgtgctgccttgacacgtcacattaattc-----tagtccat---gaaattttgccagGAGGTGCCTA-GTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G342588_T01 (Zea mays), 3'ss of exon 3
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                          ||||  |  ||||    |||  || | ||  ||  | ||| |  |    || |  ||||     ||  ||||| |||  | | |   | || ||     | |  | |  | |||     |  ||||  |      |||||| |||||||| |||||||||||||| |||||||| || ||||| || ||||| || || ||||| ||||   
-----------------------------------------attttatgtttgat----ttacttctatttgattcagttgaaatatttctttatatgtttcatatattgtttagctaatct-tagca-acttgaaccggctatcagGATGCTGGAGCACTACCTTCACATCC----AAAGCATAATAAAGGTTGTCACTGCAAGAAGTCAGGTTGTCTAAAGAAATACTGTGAATGTTTTCAAGCGAATA---

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                              | |||||||| |  |   | ||| ||   |||  |||| |||  ||  ||  |  | |||| | |   ||| | |      |  | | |  |||       | |||   |   | |    | |||   |  || | | | |  | |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||| ||||| |      
-----------------------------aatgtgttatttccctaaag-atg-tgaaatta--tcaattttcatg-aatattgataactgatttacttttcttt-----ctgggctgaactgt-------tcaaaa--cgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                   | ||   ||||  | |   | |      ||    |||||   ||   | |       |||||||   |     ||||  |  ||||  | |   | || | |||       | |  | |||  |      || | |    || || ||||| ||||||||||| ||||||||||| || ||||| ||||||||||| || ||||||||||| |      
-----------------------------------tcatgtattttctgta--gtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagt---ggatttcgg--aactaataga--actttattattgcagGAGGATGCTGGAGAGCA----TCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA------

upper sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatac--ttactgttctgggtttatctga-tattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
                                               |   |  | || ||    ||| || | |   ||  |    ||| | ||||     |    || |  || |   ||||  |||     ||   |||       | |    |||  |      ||   |    || |||||||| |||||||| ||||| || || || || ||||| ||||||||||| || |||||||||||||      
----------------------------------------------cgtattccttctgttgtaccaaattatattccatagtttcattatttttcttaacctgggcgagtggttgacgaaactgatggcat-cttggttattgcagGAGGATGTTGGAGAGCA----TCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCA------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
              agttaac  putative branch site (score: 3)
                                       tcttgttt  putative PPT
                              atttaaatatcttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT