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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaacattgttatttgctcttaatgtcttcctgacggcaaaaatgcagacaaccaactggaaacttcgctgtggttttgccagtttttcagtgacaacatcatatatgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG

Basic information

species Zea mays
transcript GRMZM2G092459_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 8
gtacaaacattgt-tatttgctcttaatgtcttcctgacggcaaaaatgcagacaaccaactggaaacttcgctgtggttttgccagtttttcagtgacaacatcata-tatgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG
|||||||| ||   | ||||||||   | ||| |||||  ||| ||   ||     | |||  |||||||   |||| | |||  |  ||   ||  ||| |  |||  | |   ||||||||||| ||||||||||| ||||| || || ||||||||||| |||||||| || ||||||||||| ||||||||||| || || || ||||||||||||
gtacaaacttttcatgtttgctctggctctct-cctgattgcagaagaacactggccaaaccagaaactttattgtgatattgg-aacttggaagctacagctacattctgtttatttcagGCCCAACCTATAGAAGTAAATGTAGTTAGCCATCCTATTCAAAGATATGCTGTCTGGTTTGGTGGTTCTGTGCTTGCCTCTACCGCTGAATTCTACGAG
















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|12969341|gb|BG266285.1|BG266285
EST:     GTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: GTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
EST: gi|50332365|gb|CO527491.1|CO527491
EST:     ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
EST: gi|5058743|gb|AI737219.1|AI737219
EST:     ATGCNCGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
EST: gi|50332358|gb|CO527484.1|CO527484
EST:     ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
EST: gi|31441053|gb|CD510484.1|CD510484
EST:     ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTG
genomic: ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTG
EST: gi|31406260|gb|CD484992.1|CD484992
EST:     ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAG                         GCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG
genomic: ATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCG

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), 45 (downstream exon)
Score: 67

GTTTAAAGATTTCCATAGGAGGTTACAGCGGGACCTCAAAAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 14

GTTTAAAGATTTCCATAGGAGGTTACAGCGGGACCTCAAAAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

GTTTAAAGATTTCCATAGGAGGTTACAGCGGGACCTCAAAAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG


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

GTTTAAAGATTTCCATAGGAGGTTACAGCGGGACCTCAAAAAGATAGTGGATGCACGGGTCCGTGCATCTAATAGTCGGCTTCTTAGTGGAGATGCTAAGgtacaaacat ... tgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttcgctgtggttttgccagtttttcagtgacaacatcatatatgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG
                                                ttttc  CT-rich tract
                                     atcatatatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaacattgttatttgctcttaatgtcttcctgacggcaaaaatgcagacaaccaactggaaacttcgctgtggttttgccagtttttcagtgacaacatcatatatgattttcagGCCCAGCCTATAGAAGTGAATGTGGTCAGTCATCCTATTCAGAGATATGCGGTATGGTTTGGTGGATCTGTGCTTGCTTCAACTGCCGAATTCTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA