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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT

Basic information

species Glycine max
transcript GLYMA02G00510.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                |  | ||     |||  ||  |   ||||    |     ||||   | ||  || |   | |   |  ||    |  ||||||| ||||||||||||||||| ||||| || || ||||| || || ||||||||||| |||||| | || || ||||| |||||| | ||||| |  |
---------------gtaaggctgagcatttctatggttacatggccatcattttttttttaacctcttaccctctctaataa-gctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14
gtacacttatgatccatttgtcttg-attttttaatattgcaatggttca-cgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                |  |  ||  |   ||| ||   | | |||  || |||   |  |  ||     | | | |  |    |||   ||| |||||||| || ||||||||||||||||||||||| |||||||| |||||||| |||||||||||||| || || ||||| |||||||||||||| ||||  |
---------------gtaaggattatacacttttatcaagtagtggagcatcgaaattcattatactcagtttttttctt----ttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12
----------gtacacttatgatccatttgtcttgatttt-ttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
           |  ||| ||       ||      |  || ||  |  |  | |||||   ||||   || || |||||||   |||||   |||   |  | ||||| ||||| ||||| |||||||||||||| || |||||||| || || || |||||||| ||||| ||||||||||| ||||||||||| ||||| |  |
gtaaaatttctttaactgatatcatgcttcctagaaccttgtttttcctaaagtggttattgaggaactttgttgctgata--gattgttgtatt---aattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 15
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatc-tattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                                                | |  | | ||    ||||    | |      |||||||  | |||||||||| ||||| ||||| ||||| || |||||||| ||||| || ||||| ||||||||||| ||| | || ||||| ||||||||| | ||||| |  |
----------------------------------------------gtatgctgctctt--ccgctgcagccgtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 14
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                                      | ||  ||  ||||   ||||  |  |   | ||| |     |  |||    || ||||||| || ||||| || ||||| ||||| |||||||| || ||| |||| || ||||||||||| ||||| ||  | || ||||||||||| ||||  |
--------------------------------------gtaa--gtgtacga--tttttcttttcgtgtgtctctcaataagctgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTAACGAAATACGCAGGTCTAGTCTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACAT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 15
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatc-tattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                                                | |  | ||||    |||    || |      |||||||  | |||||||||| ||||| ||||| ||||| || |||||||| ||||| || ||||| ||||||||||| ||| | || ||||| ||||||||| | ||||| |  |
----------------------------------------------gtatgctgctttt--ccgctacagtcgtgaaactcaattgctgt-tatagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                                      | ||  ||  ||||   || |  | |    | ||||         |||    || ||||||| || ||||| || ||||| ||||| |||||||| || ||| ||||||| ||||||||||| ||||| ||  | || |||||| |||| ||||  |
--------------------------------------gtaa--gtgtacgatttttcttttcgtgtgtctctaaataagctgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT

upper sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 14
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT---------------
                                                    |  ||||  |  |   | ||| |     |  |||    ||  |||||| || ||||| || ||||| ||||| |||||||| || ||| ||||||| ||||||||||| ||||| ||  | || ||||||||||| ||||  |               
------------------------------------------------gtacgatttttcttttcgtgtgtctctaaataagctgcctgttaccggttgtcgcttctcagGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACATGGGTTGATCCTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT
                      agctgat  putative branch site (score: 4)
                           atatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttatgatccatttgtcttgattttttaatattgcaatggttcacgagggttttggtagctgatatctattgtgcaattgcaatctatagGTTGTAGCATCTCAAGACTGGCCTGAAGTGACGAAATATGCCGGTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA