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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgagatgtgcatcaagtcatcaacatacaggaagattccatgtgaatagtctgagattactattaatttcacaattatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 6
---------tgatgagatgtgcatca-agtc--atcaacataca-ggaagattccatgtgaatagtctgagattactattaatttcacaattatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG
          ||  | || |  || | |||   ||||||   || |||| ||||||  | ||| ||||||||         || |||    |||   |   ||   ||| ||||||||||| || ||||||||||| || |||||||||||||||||||  ||| |||| || |||||||  |||||||| |||||||||
gatgagagcagagaaaatatatatgagagttgtatcaactggcatggaatattccaaat-aatggtctgagac-------gatctcatg--tatccct---atgtttgtgcagGAGATGGAAAATCCTCTTATTCTAATTCATGACAAGAAAATCTCAACGATGAATTCACTTCTTCCAGTTTTAGAAATGTCTATCAAG

upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01190.1 (Glycine max), 3'ss of exon 6
---tgatgagatgtgcatcaagtcatcaacatacaggaagattccatgtgaatagtctgagattactattaatttcacaa--ttatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG
   |||  | | ||   |    ||||    | |  |    | | ||||  ||||     |   | |  | |||||    |  ||  ||  ||   |  |  | ||||  ||||||||||  ||||||| ||||||||||||||||| ||| ||||  |||| || ||   |  | | ||  |  || | | |
atttgacaaaa-gtatctttgttcatttcaacat-gatgcacttcatgcaaataa---aaagcttcattcaatttggttaactttcttaattttaattttattagGAATTGGAGAACCCCTTTATTCTCATCCATGACAAGAAAATTTCAGACATAAATTCACTGCTGAAAATACTGGAGCTGGCTGTAACG

upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20560.2 (Glycine max), 3'ss of exon 5
tgatgagat--gtgcatcaagtcatcaacatacaggaagattccatgtgaatagtctgagattactattaatttcacaattatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG
|||||   |   ||||   |   | |  ||| ||    | ||   | |   | |  | ||||   | | |  || | ||   |   ||| ||   |  ||||||  ||||||||||  ||||||| ||||||||||||||||| ||  ||||| ||||  | ||   |  | | ||  |  |  | | |
tgatgcacttcatgcaaataaaaagcttcattcaatttggttaattttctttgggttcagatgtgtgtgatattaataagggtaattttaat--tttgtcagGAATTGGAGAACCCCTTTATTCTCATCCATGACAAGAAAATTTCTGACATGAATTCATTGCTGAAAATACTGGAGCTGGCAGTAACG

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|18450792|gb|BM429070.1|BM429070
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAAATCTCAAACAT
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAA-TCTCAAACAT
EST: gi|149014572|gb|EE044215.2|EE044215
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|71438972|gb|DR820022.1|DR820022
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|18649393|gb|BM498212.1|BM498212
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|18649481|gb|BM498300.1|BM498300
EST:     ACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: ACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|78118616|gb|DV537000.1|DV537000
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTTCTTATC
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATT-CTTATC
EST: gi|18649617|gb|BM498436.1|BM498436
EST:     GAGGATACATATCTCCTTACTTTGNGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GACATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|6021191|gb|AW066119.1|AW066119
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|18450399|gb|BM428677.1|BM428677
EST:     GAGGATACATATCTCCTTACTTTGNGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|87153562|gb|DY398351.1|DY398351
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|18648744|gb|BM497563.1|BM497563
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|67015320|gb|CO444069.1|CO444069
EST:     GAAGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACA-GAAAATCTCAA-CATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|149010196|gb|EE042014.2|EE042014
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATG
EST: gi|31664231|gb|CD572956.1|CD572956
EST:     GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGT                         GAGATGGAGAACCCTCTTATTCTTATCCATG
genomic: GAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGAAATGTgtaagtctgc ... acctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatagtctgagattactattaatttcacaattatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG
                                              cctgttc  CT-rich tract
             attactattaatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgagatgtgcatcaagtcatcaacatacaggaagattccatgtgaatagtctgagattactattaatttcacaattatttgtttgatacctgttcagGAGATGGAGAACCCTCTTATTCTTATCCATGACAAGAAAATCTCAAACATGGATTCTCTCCTTCCAGCATTAGAAATTTCTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - -gtgcatc
- - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - -catgtga