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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatactgtttgccaatatctatgtggtatgatatgctttgatatgtaaactgagtaactgacaaacttcactgtaaccttttctttctctaaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG

Basic information

species Zea mays
transcript GRMZM2G179429_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 5
gcatactgtttgccaatatc-tatgtggtatgatatgctttgatatgtaaactgag--taactgacaaacttcactgtaacct--tttctttctctaaactt--cagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG
      | | | |  ||  | |  || |||| |  | ||| | ||      ||  |  ||    ||  ||     |||||  |  ||| ||||  ||||| |  ||||| |||||||||||||| ||||||||||| || ||||||||||||||| |||| |||
------tatattctcatgccgttggttgtataa-gtacttaggtaaacctgcttggcttagtaaactgacaattttgtaattttatttgtttccataaaccttacagAACCAGAAGTGTGTTCCTCTAGAGGACCTTGCCGCAGAGTTCAGGATGAGAACACAG
















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|50329493|gb|CO524619.1|CO524619
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAG
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAG
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|76014913|gb|DT942083.1|DT942083
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|76014912|gb|DT942082.1|DT942082
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|32165071|gb|CD670389.1|CD670389
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|148956262|gb|EC902060.2|EC902060
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCCG
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGC-G
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|31364620|gb|CD448975.1|CD448975
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|78112542|gb|DV530936.1|DV530936
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAAAAGTGTGTTCTCCCTAGAGGACCTACCTGCAGAGTTCAG
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTC-CCCTAGAGGACCTAGCTGCAGAGTTCAG
EST: gi|211469382|gb|FL187167.1|FL187167
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGT-GAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|71307153|gb|DR789747.1|DR789747
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|211427421|gb|FL445183.1|FL445183
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATATATCAAG                         AAGCAGAAGTGTGTTCCCCTAGATGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|71757661|gb|DR955598.1|DR955598
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGA
EST: gi|148959747|gb|EC905644.2|EC905644
EST:     CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAG                         AAGCAGAAGTGTGTTCCCCTAGAGGGAC-TAGCTGCAGAGTT
genomic: CACAAGACGATGGTCAGGGTTTGCTCCACAACTTTGTGGAATACATCAAGgttatgaagc ... taaacttcagAAGCAGAAGTGTGTTCCCCTAGAGG-ACCTAGCTGCAGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaactgagtaactgacaaacttcactgtaaccttttctttctctaaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG
                                ccttttctttctctaa  CT-rich tract
                                  ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatactgtttgccaatatctatgtggtatgatatgctttgatatgtaaactgagtaactgacaaacttcactgtaaccttttctttctctaaacttcagAAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG