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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

Basic information

species Glycine max
transcript GLYMA07G38050.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 7
----ttgaaatctgaattt-ttttccttttcatttgttgcataggt--aagtgataatgttaataca----cttaagtaattaat-------------gtgatttgtttctt------ttgacgtt-gcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
     |     |||  | |  | |  ||||    ||| ||   |||  |||| || |||||  |  |    || ||| | ||  |              | ||| |||  |       |||| ||| |||||| ||||| ||||| || ||| |||| ||||||||  | ||||||||||||||||| ||||||||||| |||||||||||||||||||| ||||||||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacatcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 7
----ttgaaatctgaattt-ttttccttttcatttgttgcataggt--aagtgataatgttaatacac-----ttaagtaattaat-------------gtgatttgtttctt------ttgacgtt-gcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
     |     |||  | |  | |  ||||    ||| ||   |||  |||| || |||||  |  ||     | ||| | ||  |              | ||| |||  |       |||| ||| |||||| ||||| ||||| || ||| |||| ||||||||  | ||||||||||||||||| ||||||||||| |||||||||||||||||||| ||||||||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacattcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------ttgaaatctgaatttttttccttttcatttgttgca---taggtaagtgataatgttaatacacttaagtaat---taatgtgat--ttgtttcttt--tgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                             |  |||| |     | ||||   |  | || | | |   |   | |||    || |    |   | |||| ||    ||| | ||      |   ||  | | | ||||||| |||||||||||||| ||| |||||||||||||  | ||||||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||||
gtatgttagcaccaccttgtcacattaattctacattgctacctatgcaaattttgtactctttctaatctaattatggtaatttgcttcagtatacatttcttcaagttcaagttatgtccaattttatcaccactgacttgattatgctgcagAATAATCTTCATGAACTTTGGTCTCTTCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAGACTTTTGATGATTGGTTCCAAATCTCAGGGGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
---------------------ttgaaatctga-atttttttccttttcatttgttgcata---ggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttct-------tttg-----acgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                     |||  || |    | |    ||    || |  |||  ||     | ||| |   ||||    ||  | |||  ||  | | || || ||||       ||||     || | |||||| ||||| ||||| ||||||||||| ||||| ||  |  | |||||||||||||| ||||| ||||| |||||||||||||||||||| ||||| ||||
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgtt--aatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                             | |||   ||| ||   | ||  |||| |    |  | |     |  | || ||    |  | |    |   || | ||||||| | ||    || | |||||| ||||| ||||| ||||||||||| ||||| ||  |  | |||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatc-ctagtctgatttgctgct----acatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------------------------------------------------ttgaa-atctgaatttttttccttttcatttgttgcataggtaagtgataatgttaat------acacttaagtaat-taatgtgatttgtttcttttgacgt-tgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                                                                       ||| |   ||   |||     |||  | |||| |     ||  | |  |||| || |       |    |  |||   |  |||  |    || |  | |  | ||||||| ||||| |||||||| ||||||||||| || |||||| ||||||| || |||||||| || || ||||||||||||||||||||||| |||||||| |
gtgtttgctctatcttattcttgaatatttggacattgaagttttctttgttaagttgcttctaattgaatgttgaaacaacctttcttgtacggctctgtttgcactcttaacttttgcttttccgggcacttttaatatttaccgtataatgactgtgtagcctgctgtactcatattgtcctcatatatgcagAATAATCTCCATGAACTGTGGGCTCTTCTAAATTTTCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgac---gttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
 |    | |   ||  | | | ||  |  || | | ||  ||  |  |    || ||   ||| ||| | || ||| |||  |||| | ||       | ||||| ||||| |||||| | ||||| |||||||| |||||| | |||||  | |||||||| || ||||||||||| || ||||||||||| ||||||||||
-ttttttttcttttcgtgttccttagacatgcttcttac-tatcttctgtacttgatttgcttgagttaatattgt-attcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 7
----ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgt-tgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
    || | || |  |  |  | | | ||    | |   |||   || | | ||||  || |   |  || |  | |  |  ||  | |||||||   | |||||||||||||||||||||| ||| ||||||||||||||||  |||| || ||||||| ||| ||||| ||||||||||||||||| ||||| ||||| || |
actctttatatatacacatact-cttatttgcctatccaataa--aaataaaaatg--aaaatggtgtagcatgtgacatccttgctatcttttgctatgtgcagAACAATCTTCATGAACTATGGTCTCTTCTCAACTTTCTACTGCCCGAGATATTTAATTCAGCTGAGACTTTTGATGAATGGTTCCAAATTTCTGGAGATA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                       |||  | | || |||      ||||||   | ||  | |||   |    |    |   ||||||||||| || ||  | ||||||||||| ||||||||  |||| || || || || ||||||||||| || || |||||||||||||| ||||| ||||
---------------------------------------gtattttaaaaggttt-----cttaagc--tgaacctaattcactgaactgattg--acagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 6
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                       |||  | | || |||      ||||||   | ||  | |||   |         |   ||||||||||| || ||  | ||||||||||| ||||||||  |||| || || || || ||||||||||| || || |||||||||||||| ||||| ||||
---------------------------------------gtattttaaaaggttt-----cttaagc--tgaacctaattcactgaaccgattg--acagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
                                         ttttgac  putative branch site (score: 3)
                                     tttcttttg  CT-rich tract
       ttaatacacttaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

- - - - - - - - - - - - - - -tgttgca