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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC

Basic information

species Zea mays
transcript GRMZM2G017835_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 13
-----ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC-
     |   |   |   |       || ||| |    ||     |    |||      | | | | |  || |||||    ||   || | |  || |||  |||||||||  |||||||| ||||| || ||||| ||||| || || ||||| || |||||||||||||| |||| ||||||||||||||||||  ||||||| 
accaagaatccaatatatgaatttctgcagatctctacatacaagcat-tctgctgttgctaactctaatttttggtgacttg---tattctaatttatg--caggCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACCTCAATGGCC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 13
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacag--attagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
  | |||||  ||   |   ||     |     ||   |     |  |   |||  | |  |   | || |  |  | |||| ||  || |    |   |||| || |  ||||| || |||||||| ||||| ||||| || || || || || |||||||||||||| |||| ||||||||||||||| ||| |||||||
--tgcttttgtttgaacacgtgggtttctgaagacctctacatataatgctcagcaactgttacctctgattttgttgtgatttatgatctaatttctgcagGTACGCAGTATACTCAACAATCTTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgt----ctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
    |||||  ||   |  ||| |   |     ||   |     |    |||   || | |  |   | || |  |  | |||| || ||| |    |   |||| || |  ||||| || ||||| || ||||| ||||| || || || || || |||||||||||||| |||| ||||||||||||||| ||| |||||||
---gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgca-actgttacctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 11
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttg--ttggtcctctgatatagtatgtttga---tggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
     || ||     |   || |  |      ||    | | | |    | ||   |  | ||  |   |  |   | || |    | || |  |   |   |||||||||  |||||||| ||||| || ||||| ||||| || || ||||| || |||||||||||||| |||| ||||||||||||||||||| |||||||
----tttctttggaccaagatatgaatttctgcagatctctacatacaag-cattctgctgttgctaactctgatttttggtgacttgtggtctaatttatgcagGCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACTTCAATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
ggtcctttttcttttc-cgaatg----tagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttga------tggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
 ||   |   ||||||  ||||     |  || || ||   ||| || || ||| ||   |   |   ||||| | |  |   || |    | ||  |      |    ||| || |  ||||||||||| ||||| ||||| || ||||| || || || |||||||||||||||||||||| |||||| || ||||| ||  |||||||
-gtatctacacttttcatgaatacttttgaacactttcgtcattatg-gtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 13
ggtcctttttcttttccgaatgtagaccctg---tcacgattgtgcgtctttgacagattagtttt--tttgttggtcctctgat-atagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
    | | ||    |    |    ||   ||    | |  |||    | | ||  || ||| |||       ||  || | |||  |||      |  ||   ||||||||| |||||| || || ||||| ||||| || || |||||||| ||||| |||||||||||||| |||| |||||| || ||||| ||| | |||||
---acctatttacatgaagacactgattatgagtccccagttgctaatttatggtag-ttattttcagccactttatcatttgaccataaccaaat--atctgcagGCACACAATATACTCAACAGTCTTACAAAGTAAGCGACTCCTTTCCCTTTAAATGGATAAACAAGAAGTGGAGAGAAGGATTCCATGTAACTTCCATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcct--ctgatatagtatgtttg-atggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
 ||| |  | |||||   ||| |      | |    ||| |  || |||||   ||| || |   | || ||  |  || || |      ||||  |   |||| ||| ||||||||||||| || || ||||| ||||| || ||||||||||||||||| || |||||||||  |||||| ||  | || ||  | |||||
cgtcatagtccttttt--aattttagttattttttaatttttagt-tttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------------------ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
                                                                             | ||| |  |||  |   || ||||| | |   | || |  | || |      ||    || |||   |   ||| |    || | |||  ||   ||| ||  | || || ||||| ||||| ||||| || || || ||||||||||||||||| || |||||||||  |||||| ||| | |||||| |||||||
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttg----ttttacttgttgcatgatgtctcacggtgtttatttc-tg--tagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|6020774|gb|AW065582.1|AW065582
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|67011551|gb|CO440300.1|CO440300
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|16918498|gb|BM073773.1|BM073773
EST:     TGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|32940878|gb|CF045697.1|CF045697
EST:     TTCTGTTGCTGGCTCCAGCAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|213179378|gb|FM182943.1|FM182943
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|148939515|gb|EC884103.2|EC884103
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|6020754|gb|AW065562.1|AW065562
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|76285883|gb|DV025451.1|DV025451
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|38568968|gb|CF974853.1|CF974853
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|67025680|gb|CO454429.1|CO454429
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|211501406|gb|FL138832.1|FL138832
EST:     CAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: CAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|67025667|gb|CO454416.1|CO454416
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|67011858|gb|CO440607.1|CO440607
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|113702247|gb|EE679751.1|EE679751
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|14204221|gb|BG837898.1|BG837898
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|33101699|gb|CF061659.1|CF061659
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
EST: gi|211123481|gb|FL438361.1|FL438361
EST:     TCTGTTGCTGGCTCCAACAATGGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCCATATACACCAGCAATCTTATAAAGTCAGTGATTCCTTTCCATT
genomic: TCTGTTGCTGGCTCCAACAAT-GGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACA-CCATATACA-CAGCAATCTTATAAAGTCAGTGATTCCTTTCCATT
EST: gi|31359524|gb|CD443881.1|CD443881
EST:     TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG                         GCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA
genomic: TTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAGgtataaatgt ... tgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
         attagtttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG