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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

Basic information

species Zea mays
transcript GRMZM2G354532_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
-----------------------------gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                             |   | |      || |  |  | |    |   | | | |||| |          ||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
------------------------------gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                              |   ||||||     |||    | |||  |||   | ||  || |      |  | |||||||||||||||| ||||||||||| || ||||| || || ||||| || ||||| || || |||||||| ||| |||| |||
gtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaa-aatatggttttgtttgttgc-agTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 18
-------------------------gtatt-atttcacct--aatgggcaactgatgagattcactactgtctcaagGCTAAC------CAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                          |||| || ||||||  | | |    |||   | ||  |||  |||       |          ||||||||||| || || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||
gttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
-------------------------gtatt-atttcacct--aatgggcaactg---atgagattcactac--tgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                          |||| |||||||||  | | |    |||   ||   | ||| |    || |||         |||||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||
gttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
-----------------gtattatttcacctaatgg-gcaactgatgagattcactactgtctcaagGCT--AACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                    |||  | ||   || | |       ||||||| |    || ||  ||  |      ||||||||||||| || |||||||| || || |||||||||||  |||||||||| ||||| || || || || ||| ||||||||
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagatt-agacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------gtattatttcacctaatgggcaac-tgatgagattcactactgtctcaagGCTAAC--CAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                            |     |     |     |     |  ||| | |   |    ||   |   |     ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||||| ||||| |||||| | ||| |||| |||
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG

upper sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
----------------------------gtattatttcacct----aatgggcaactgatgagattc------actactgtctcaagGCTAAC----CAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                             |||   || | ||    | ||||    |  |    ||        ||  | |||||    |       ||||||||||| || || ||||||||||| ||||| ||||||||||| || |||||||| || || |||||| ||||| | ||||| 
gttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                           aactgat  putative branch site (score: 3)
                                             ctgtctc  putative PPT
       tattatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG