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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt...

Basic information

species Glycine max
transcript GLYMA09G41510.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccatta-tgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt------
 ||| |||||||||| ||||| |||||||||||||| || |||||||| ||||| |||||| | |||||||| ||||||||| | ||||| ||||||||||   ||   || |         |  | | |||  ||    || ||||   |  |  || |  ||  || ||| |||          | |  ||      |       
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgcaagacattttttcca-----tccagctattcaagatgctagtgttttttttttgttat--ttgagtggtaagttggtaaccgactctccaaatgatggcaaaata

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 9
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccatta-tgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt---
 ||| |||||||||| ||||| |||||||||||||| || |||||||| ||||| |||||| | |||||||| ||||||||| | ||||| ||||||||||   ||   || | |   |      | | |||  ||    || ||||   |  |  |  |  ||  || ||| |||      |   | |  ||      |    
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgcaagacatttttttccatcc----agctattcaagatgctagtgttttttttttttgttatttgagtggtaagttggtaactgactctccaaatgatggcaaa

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G460090_T01 (Zea mays), 5'ss of exon 1
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggct-cataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt----
 ||| | ||||| || || ||  |||| || ||||| || |||||||| ||||| |||||  | |||||||| || |||||||| || ||||||||||||||  |    ||  |||    |       |||   || ||  || ||  ||  | ||| |   |||  ||       || | |  ||| |  || | ||| |    
AAGTCCTTTTTTTACGGAACAACTGACGGCTTTTGAAGTGTGGCTTGATCATGGCTCTGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTCAGgtaaggcattttgctta---tacacttacatacaagtca--atattatctgtaaaatccagtttaactttgtaacctcttcacctttctctaagctgctatggtt

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgc---gatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt
 ||| | ||||| ||||||||  ||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||| || ||||| ||||| |||||||||||||   |||   |||  |  ||||         | |||  |    |   |      ||||   ||   |||    ||||    | |  ||    |  |    
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgct-gagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga--

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtg-atttttgtgaaatcagctgt
 ||| ||||||||||||||||  ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||||| | |     | |   |||      | | ||    |  | |  ||| | ||  |   | |   |   |   |      || | | ||  ||     | 
AAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTCAGgtgccacctgaaccctaaatttacccctcctgtgttttaa-aagaaggcccctatcttatggtccatgagaaactattcatatctatttgtcattcatcga

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt--
 ||| | || |||||||||||| |||| || |||||||||||||| || ||||| || ||||| |||||||||||||| |||||||| || |||||||||||  |||  ||  |||| ||  | |||      |  |  |  | ||||    |  || |       || ||  | | ||| |||||  | |      | |  
AAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTCAGgtaggatattttccttgattcctataaattccaggactgtagt-ttggtctttgttttttccccccttatat-tatggtggtttttaagtatatttttatgg

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgta-accatttgagccattatgttggctcata-attctcgttaggt-tgtaggtttcgtgatttttgtgaaatcagctgt
|||| | |||||||| ||||| |||||||| || ||||| ||||| || ||||||||||||   ||||| ||||| || ||  | ||||| |||||||| ||    |  |  ||  |   | |    |    |    |     | |      ||  || ||| | |     ||||  || | ||  ||| |||  |    | |
TAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTCAAgtatagtg-tgatcaagccatctaagtagtgctcagactggagtatctatggatgcatgctcatgaaaaacgtag--ttagcgacgtttctgatgttctgtat

upper sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 5'ss of exon 10
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgt-aaccatttgagccattatgttggctcata-attctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt
|||| | |||||||| ||||| |||||||| ||||| || ||| | |||||||||||||| |  ||||| |||||||| ||| | ||||| ||||| |||||    |  |  | | |   | ||  ||  | | |  |    ||   ||  | ||  |    |||   | |  ||||| ||     | ||  | |  | |  
TAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGCAGgtatagtg-tgatgtagtactgtgccaataagtagtactcagattcaggtacctatgtaggagttttttggagggtttagtttgcgtcgttgactatgttc-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgcgatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA