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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

Basic information

species Zea mays
transcript GRMZM2G353548_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
aatgatttgcttattatcctccacaactactcatattgctcata--ctttgtgtacaat-gtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
  | || || | |||     |  |   | ||  |    || | |  ||  ||    | |  | |   || |  | |     || ||   ||| || || |||||| |||||||| || || |||||||| || ||||| ||||||||||| ||||||||||| || |||||||||||||||||||  || |||||||| ||||
--tcatgtgttaattgcttgctccggtttct-gtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
aatgatttgc-ttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatca-atctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
   |       || || || | || |   |   ||     |  |    |    |   | | || |  | | | |  |||||   |||  ||| |   |||||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||||| |||||||| |||||||||||||||||  | ||||| || || |
gccggcacaaattgttgtcattcata-tcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtc-ttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
aatgatttgc-ttattatcctccacaactact-catattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
  ||       || ||  | | || | |  ||      |  |  || ||    |    | ||| |  || |     ||| |   |||  ||| |   |||||||||| | ||| ||||||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||||||||||||  | || || || || |
gctggcacaaattgttgccattcatatcatctatgccctttttgtagttcaaatg-gttttaatctgaatttaatgtctatgaatttgctttgtc-ttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------aatgatttgcttat--tatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                              |||| || ||  ||   ||  |  |  | ||   ||||     | |||| |  ||  ||  |||  |   ||       |||||     | |||| ||| || | || ||||||||||||||||| || |||||||| ||||| ||  | || |||||||| |||||||| |||||||||||||  || || || || ||||
gtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtttagcagatgccattttatatcattaactatat-----acacttggaatatcatacaag--agtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
aatgatttgcttattatcctccacaactactcatattgctcatac-tttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                        ||   || ||  | ||  ||| |   ||| ||      |   |  || ||      || |||   |       | || |||| ||||||||||||||||||||||||||||| || || ||| | || |||||||| || ||||| || ||||||||||  || ||||| || ||||
----------------------gtaaagccttatgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
----aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
    | | || |  | |||||       ||   ||   |||  | ||   || | |    | ||    |   | ||||  ||     |   ||||| | |  |||| || |||||||| |||||||| ||||||||||| ||||||||||| || ||||| || ||||| || |||||||||||||     |||||||||||||
tgctacttatgttgtgattataggaataaaactcttggattttttatttatttttttatttctatttta---tttcaactttcaaaatatttttatca-tgcagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------aatgatt-tgcttattatcctccacaactactcatattgctca--tactttgtgtacaatgtaagccaaactatc--aatcttt----ttttttaatttattact-----ttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                               | | | | || |  | |   ||  ||| |     |  || |||  |||||| |   |  |  ||  |  ||| |    ||||||    | |   |   | ||  |     | |||| ||  |||| ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||| || ||||||||||||||||| ||||| || ||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaa-gtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                                                ||  |||||    | | | ||     ||| |  |  ||||         |    ||| | |      | | | | || | | | |  | | ||     |||| || |||||||||||||||||||||||||| ||  | |||||||| |||||||| || ||||| || |||||||||||   |   || ||||| ||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagtt-cta-tattcctgcttgattcagttaagtaattttacttgggccaacca-ctgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

upper sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgc--tcatactt-tgtgtacaatgtaagcc----aaactatcaatc--tttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                                                  || ||| | |     || |    | |    ||  | |  || |||||  ||  | ||   || |       ||||   |    |||| | ||  | | ||   | ||||||| ||||||||||||||||||||||||||||| ||||| ||||| || |||||||| ||||| || || ||||||||   |   || || || ||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG
                                    ttttaat  putative branch site (score: 3)
                                              ttacttt  putative PPT
                   aaactatcaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgatttgcttattatcctccacaactactcatattgctcatactttgtgtacaatgtaagccaaactatcaatctttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

- - -tttgctt
- - - - - - - - -cctccac
- - - - - - - - - - - - - - - - -tattgct