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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

Basic information

species Zea mays
transcript GRMZM2G032367_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6
-----ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
     ||    |  | | || |||||  ||  ||   || | ||    ||||| ||    |   | |||   |  |  |||  |  |||||||| ||||| |||||| ||||||||| |||| ||||| |||||||||||||||||||||||||| |||||||||||||| |  |||||||||||||| ||||| ||||||||||
gttatttttctagctgtaatttttcaagctggttgtgttctgtt---atttgctttctgcagtgtgcaac--attagtaaactctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
ttaaggatgtattatctttcatactcttttccttttttttgtgtttgc--ctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
       |  ||| ||| || || | ||| | ||    ||||  || |  ||| |   | ||  |||| | || | ||  |  ||  | |   |||    ||||  | ||||| || |||||||| || || ||||||||||| || || || ||||| || |||||||| |||| |||||| || ||||| ||||| ||||
------gtaaatt-tctctcctatt-tttgctttagacttgttattacaacttcaaattgttggaagtta-gaaataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 5
ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataa-aaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
                     ||   || ||   ||||     ||   |||       ||  ||||   | | |  ||| ||  | ||||   | | | ||||| | |||||  | |||||||| || || |||||||| || || || || ||||| || ||||||||||||| ||||||||||||||| ||||||   |
--------------------gtaagtttctctcattttccacattgaacttcttcgaattcaaagtgctggttatgaaaaatccgatgataactgtac-agATTAGAGAGGGGTTACACTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
ttaaggatgtattatcttt-catactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattg--gttgatctgtatcc-tagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
     |||  || |||||  | |    |||  | |  |||  |   |   | | |  ||||  ||  || | |  |      ||   |||| || | ||  |||||||| || || |||||||| || || || ||||||||||| || ||||| |||||||| |||||||  ||||| |||||||||||||| |||||||| |
---ccgata-atcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5
--ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
   | |   | | |||| ||| ||  |  |   | | || | ||   ||         || |  |  |||  |   ||    ||     || | | |  ||||| || || ||  |||||||||| || ||||||||||| ||||| || || ||||| || ||||||| |||||| ||  |||||||||| |||||||| |
tgctgatttttttttattttttatgtttatggacatattct-gttcatgatgacctattcctctacctaatcaatcaagttgttcacaaatattt-ttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

upper sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
lower sequence: EDO96204 (Chlamydomonas reinhardtii), 3'ss of exon 7
--ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttacta-tcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
  ||||  |   || |  | | |  | |           | |     |  | | |||| || |  | | |||  | |    ||   |   | | | | |  |||| || ||||| ||| ||||||||||||||||||| || || ||||| |||||||||||||||||    || || | ||| ||||| ||||| || || |
tcttaattaatcatgaa-tgtaaccccccccaaagagggtctaccactttcgtaactaatcatgaatgcaaccctcaccctcaaccgcc-acccgga-cgcagATCCGCGAGGGCCTGTACTACAACCCCTACTTCCCGGGCGGCGCCATCGCCATGCCCAAGATGCTGGTGGACGGCGGTGTGGAGTACGAGGACGGCACGC

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|71331562|gb|DR802627.1|DR802627
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|60347964|gb|DN214937.1|DN214937
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|30705061|gb|CD058656.1|CD058656
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|50338206|gb|CO533332.1|CO533332
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|14245130|gb|BG873712.1|BG873712
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|149089338|gb|EE178570.2|EE178570
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|76290228|gb|DV029796.1|DV029796
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|76016444|gb|DT943614.1|DT943614
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|71757789|gb|DR955726.1|DR955726
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|78108501|gb|DV526919.1|DV526919
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|74239656|gb|DT647570.1|DT647570
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|78026464|gb|DV494851.1|DV494851
EST:     ATTTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTTGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|37386374|gb|CF630373.1|CF630373
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|101393980|gb|EB818923.1|EB818923
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|29947382|gb|CB816627.1|CB816627
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|91878166|gb|EB408123.1|EB408123
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|211323657|gb|FL286663.1|FL286663
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|14206642|gb|BG840320.1|BG840320
EST:     ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATACCGTGATCCACCTGCTGGTGTTCAGgtactttact ... tgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC
                         ataaaaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaggatgtattatctttcatactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattggttgatctgtatcctagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG