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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgaccttgactatttctagttaatttaaagtttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattttgtgtgttctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 6
gtttgttgaccttgactatttctagttaatttaaagtttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattt-tgtgtgttctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
                               | | ||  |   |||||     ||| |||  ||| ||      | || ||||   |   ||   || |||| |||| |||| | |  || ||||  ||| |||||||||||||||||||||||| || |||||  ||||||| || ||||| |||||||||||||||||||||||||||||||||
------------------------------ctcatgtcca---ttgctcagcatttatttttcttatttcctattttagatagcataatatttg-ggacattgatttatgtgagctgcttatttccattt-acagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAG

upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 6
gtttgttgaccttgactatttctagttaatttaaagtttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattt-tgtgtgttctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG-------------------
                               | | ||  |   |||||     ||| |||  ||| ||      | || ||||   |   ||   || |||| |||| |||| | |  || ||||  ||| |||||||||||||||||||||||| || |||||  ||||||| || ||||| |||||||||||||||||||||||||||||||||                   
------------------------------ctcatgtcca---ttgctcagcatttatttttcttatttcctattttagatagcataatatttg-ggacattgatttatgtgagctgcttatttccattt-acagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAGGTTTGCTTTAAGCATTGTA

upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 4
----------------------gtttgttgaccttgac--tatttctagt-taatttaaag--tttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattt-tgtgtgtt-ctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
                      |  ||| |  ||  ||  ||   || ||  ||||| | |  ||  ||||  ||||       |||   ||  | |||  |   |||| |    | |||| | |||||  ||| |||   || |||  |||| |||| ||||||||||| ||| |||||||| || |||||| |||| || || ||||| |||||||||| | ||||| |||||||| |||||
gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttactt-cgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG

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|37395551|gb|CF635056.1|CF635056
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     GNTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|91876014|gb|EB405971.1|EB405971
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|71765216|gb|DR963153.1|DR963153
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACAC-AAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|9953034|gb|BE639617.1|BE639617
EST:     ACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: ACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|149010068|gb|EE041875.2|EE041875
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|149108285|gb|EE292625.2|EE292625
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|111192905|gb|EE291041.1|EE291041
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|110520053|gb|EE024360.1|EE024360
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|67030403|gb|CO459152.1|CO459152
EST:     CTGCTCTTNCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGT
genomic: CTGCTCTT-CAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGT
EST: gi|37373821|gb|CF623233.1|CF623233
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCNTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|149073833|gb|EE162155.2|EE162155
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|60354415|gb|DN221388.1|DN221388
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGA
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGA
EST: gi|211139771|gb|FL315903.1|FL315903
EST:     -TTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCNGCGATATACGTG
genomic: GTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|113701058|gb|EE678562.1|EE678562
EST:     TGATTGAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: TGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
EST: gi|7844633|gb|AW787855.1|AW787855
EST:     GAATCTAGATTTTTTCCTGCTCTTCAG                         GGGGAGAACACAAAAATGTGCAGCTAGTGACGCAAATTCGGCGATATACGT
genomic: GAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGT-CAGCTAGTGACGCAAATTCGGCGATATACGT
EST: gi|71305907|gb|DR789080.1|DR789080
EST:     TTTCTTGCTCTTCAG                         GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG
genomic: TTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTG

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: 48 (upstream exon), 45 (downstream exon)
Score: 177

GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 278

GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 312

GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 172

GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAGgtttgttgac ... tttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttcatagttcaagggcatttattttgtgtgttctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
                     tttattttgtgtgttc  CT-rich tract
                    atttattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgaccttgactatttctagttaatttaaagtttaaatttgcttgtggtttctttacctttttattatatgtaaatagttcatagttcaagggcatttattttgtgtgttctttctttctttttcacagGGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA