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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgaagtgaatttgtaatttaaaaatatattccctgttgcaacctcgctgtcaggtagcaaaatgtgttttaaattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG

Basic information

species Zea mays
transcript GRMZM5G824831_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------tattgaagtgaatttgtaatttaaa--------aatatattccctgttgcaacctcg---ctgtcaggtagcaaaatgtgtttta-aattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG
                                                                  | ||  | | ||||  || ||   |        ||| | |    |    ||  |  |    | ||    |   |  | | | | |  ||| || || | ||| | ||||||||||  ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| ||
gtggttttttacagttcatttgatttatacttcagataactattgtatgttttgtaaagacatatatttttcaataaattgctatttcggatagcatgcaatttttcatgtacgacagtcatgatcttttccatcatttacttatttctcatgattgttcttcctttttctaatgcagGAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGG
















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|71445140|gb|DR826190.1|DR826190
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211252219|gb|FK953400.1|FK953400
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211156519|gb|FL164233.1|FL164233
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGAC
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGAC
EST: gi|211156514|gb|FL164228.1|FL164228
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211153314|gb|FL164202.1|FL164202
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAG
EST: gi|211252212|gb|FK953393.1|FK953393
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|74241051|gb|DT648965.1|DT648965
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|148956338|gb|EC902144.2|EC902144
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|148931204|gb|EC873960.2|EC873960
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211264909|gb|FL208725.1|FL208725
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|148952476|gb|EC898302.2|EC898302
EST:     TGGTGAGGAAAAGACGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211264914|gb|FL208730.1|FL208730
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211252214|gb|FK953395.1|FK953395
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211154915|gb|FL164213.1|FL164213
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTC
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTC
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211252217|gb|FK953398.1|FK953398
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTTGTACGAGAGACTGCTGCTGTCATGCA
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTT-GTACGAGAGACTGCTGCTGTCATGCA
EST: gi|148987620|gb|EE031494.2|EE031494
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211154922|gb|FL164220.1|FL164220
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211252215|gb|FK953396.1|FK953396
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|91875485|gb|EB405442.1|EB405442
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211158115|gb|FL164244.1|FL164244
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCTGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211252210|gb|FK953391.1|FK953391
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|32795340|gb|CD947576.1|CD947576
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211153313|gb|FL164201.1|FL164201
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GA-CATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
EST: gi|211153309|gb|FL164197.1|FL164197
EST:     TGGTGAGAAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAG                         GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG
genomic: TGGTGAGGAAAAGTCGAAAGCAGGCACAACAATATTATCGGTTGTACAAGgtatactttt ... ccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgctgtcaggtagcaaaatgtgttttaaattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG
                                     tttcatttcc  CT-rich tract
                aaaatgtgttttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgaagtgaatttgtaatttaaaaatatattccctgttgcaacctcgctgtcaggtagcaaaatgtgttttaaattattgtttcatttccaaatgcagGAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - gctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt