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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggacttcctgatttgctctccatgtcttcctgacagcaaaagaaaagggacaaccggctggaatcgttgcggctttgccagttttttagtcacacctaaatcatattggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG

Basic information

species Zea mays
transcript AC205703.4_FGT002
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 8
gtacggacttcctg-atttgctctccatgtcttcctgacagcaaaagaaaag-ggacaaccggctggaatcgttgcggctttgccagttttttagtcacacctaaatcatattggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG
||||  ||||      ||||||||   | ||| |||||  ||| ||||| |  || ||| |        |  ||| |   |||  |  ||   ||  ||| ||| ||  | ||  ||| |||||||| ||||||||||| || || || || ||||| || || |||||||| || ||||||||||| ||||||||||| || ||||| ||||||||||||
gtacaaacttttcatgtttgctctggctctct-cctgattgcagaagaacactggccaaaccagaaactttattgtgatattgg-aacttggaagctacagctacattctgtttattt-cagGCCCAACCTATAGAAGTAAATGTAGTTAGCCATCCTATTCAAAGATATGCTGTCTGGTTTGGTGGTTCTGTGCTTGCCTCTACCGCTGAATTCTACGAG
















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|84969374|gb|DW467812.1|DW467812
EST:     GGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: GGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|89249037|gb|DY620823.1|DY620823
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|4621597|gb|AI612430.1|AI612430
EST:     ATGCACGGGTCCGTGCATTTAATACCCGGCTTATTAGTGGGGATGGTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|6449711|gb|AW181251.1|AW181251
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCAATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|32920418|gb|CF025230.1|CF025230
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|74240911|gb|DT648825.1|DT648825
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|30032185|gb|CB834036.1|CB834036
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|32921953|gb|CF026765.1|CF026765
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|110210892|gb|EC892789.1|EC892789
EST:     TGC-CGGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGTTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: TGCAC-GGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|149099376|gb|EE185415.2|EE185415
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|67032896|gb|CO461645.1|CO461645
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|50336873|gb|CO531999.1|CO531999
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|28390221|gb|CB250106.1|CB250106
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|24769340|gb|CA404469.1|CA404469
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCAATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|71759494|gb|DR957431.1|DR957431
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|32920457|gb|CF025269.1|CF025269
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|32922282|gb|CF027094.1|CF027094
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|5804491|gb|AI979461.1|AI979461
EST:     ATGCCCGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|24769945|gb|CA405074.1|CA405074
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCAATCCAAAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|37382936|gb|CF628439.1|CF628439
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCAATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|32846117|gb|CD985798.1|CD985798
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|67042751|gb|CO469006.1|CO469006
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|148957989|gb|EC904154.2|EC904154
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|91872833|gb|EB402790.1|EB402790
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
EST: gi|109637254|gb|EC590799.1|EC590799
EST:     ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAG                         GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

GTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

GTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGCCGGCTTATTAGTGGGGATGCTAAGgtacggactt ... tggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcgttgcggctttgccagttttttagtcacacctaaatcatattggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG
                                acctaaa  putative branch site (score: 136)
                                                ttttc  putative PPT
                                   taaatcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggacttcctgatttgctctccatgtcttcctgacagcaaaagaaaagggacaaccggctggaatcgttgcggctttgccagttttttagtcacacctaaatcatattggttttcagGCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG