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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA

Basic information

species Zea mays
transcript GRMZM2G459437_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459437_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 14
-taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA
 | || ||||| |   ||  || |  | | |  ||| ||           |  | |||   |   |     | || | | ||||||| | |    || |||||| | || |||||||||||||| |||||||| |||||||| ||||| |||||  ||||||| |||| ||| || || ||||||||||||||||| ||||
gttagcttggtgttcttttattttgttcccactgaaaat-----------atatcactatgttctaccacttatgttttgactttttatcctttttttcagTCATCAGCTCCTGTAGAATTGACCGAAGCTGAAACTGAATATTCAGTCAATGTTGTGAAGCACATTTATGACGGGCATGTTGTGCTCCAATACAATTGTA

upper sequence: GRMZM2G459437_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 14
taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA
                | |||   |||   |       ||  ||| |  |  | |   | |    ||  || | ||  ||  | || ||     | ||||||  | |||||||| ||  | |||||||||||||| |||||  ||||||||||||| || || ||||||||| | || |||||| |||| |||||||| |
---------------gttctttcacttgattctgctccgacaattctatattttatgtagttcttttctatat-ctaaaatgtattttttt--ttaccagTCCTCAGCACCTGTGGAGCTCACTGAAGCTGAGACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: GRMZM2G459437_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 14
taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA
    |||  |  |  ||  || | || | |   |   |     ||||| |  |   |       || | ||||| | |   ||||  |      | ||||||  | ||||| || ||  | |||||||||||||| |||||  | ||||||||||| || || ||||||||| | || |||||| |||| |||||||| |
----gttctttcac-ttgtttctgctcccaca-attctatattttatgtagttcttt---ctgtatctaatgtggtatgtattttgatattttttaccagTCCTCAGCACCCGTGGAGCTCACTGAAGCTGAGACAGAATATGCTGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: GRMZM2G459437_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 14
taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactga-atctcatttgatgtgctgtaactttttgt-tcgcacttc---cagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA
    |||  | ||  |   |  |  ||| |    | ||      |||   | |  || | ||    |   |||| || |   || |  | | ||  |     |||||  | | |||||| ||  | |||||||| ||||| |||||  ||||||||||  | ||||| ||||||||| | || |||||| | ||||||||||| |
----gttattttacttagttcttgtttcaaaattatatactttatattttctttccttatatactgtaatatgtactatgtattctgatgttgctttcttatcagTCTTCAGAACCTGTGGAGCTTACTGAAGCGGAGACAGAATATGCAGTTAATGTTGTTAAGCACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA
                             ctgtaac  putative branch site (score: 3)
                                              cacttcc  putative PPT
                                taacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaggttggtatatattacttgtccttctatggaagatgagcattatggacctgactgaatctcatttgatgtgctgtaactttttgttcgcacttccagTCAGCTGCACCTGTAGAATTGACTGAAGCTGAGACTGAATACTCAGTTAATGTCATGAAGCATATTTTTGATGGACACGTTGTGCTCCAATACAACTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA