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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgattattcagctcatcatccatatccctgcatgaaattgctagctatctgtttaatcaaccagtcgatcatgcagatatgcatgctatgcatgct...

Basic information

species Zea mays
transcript GRMZM2G059191_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059191_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 5
GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgat---tattcagctcatcatccatatccctgcatgaaattgctagctatctgtttaatcaaccagtcgatcatgcagatatgcatgctatgcatgct
|||||||||| || || |  || |  |||||||| || || || |||||||| ||||| ||||| |||||||||||||| ||  |||||||||||| |     ||||    |  |||   | ||    |     ||||    | ||| |  | ||          ||| |        |   || |      |  
GTGACTTGAAGCCGGGTGATGAAGCTAAGATCACTGGACCTGTTGGCAAGGAAATGCTTATGCCAAAAGACCCCAATGCCACCATCATCATGgtatggtcatatattggcgtgctcacttagattagagagcagaatttagtggtatatagtcaacacttgtagtgattacttctgcttttctgtttccttag--
















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|71762625|gb|DR960562.1|DR960562
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71432261|gb|DR813311.1|DR813311
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|149073444|gb|EE161749.2|EE161749
EST:     TGGGCAAGGAGATGTTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71297722|gb|DR784813.1|DR784813
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71763164|gb|DR961101.1|DR961101
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|149073700|gb|EE162006.2|EE162006
EST:     AAGGGGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: AAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71306720|gb|DR789520.1|DR789520
EST:     TGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|91876931|gb|EB406888.1|EB406888
EST:     GCCCAAAGACACCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGGATTGGTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: GCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|76019472|gb|DT946642.1|DT946642
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71313358|gb|DR793225.1|DR793225
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71436411|gb|DR817461.1|DR817461
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|89248692|gb|DY620478.1|DY620478
EST:     TGGGCAAGGAGATGTTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71307167|gb|DR789753.1|DR789753
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|5928946|gb|AW056238.1|AW056238
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCCTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13178509|gb|BG349767.1|BG349767
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71326435|gb|DR799900.1|DR799900
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71428874|gb|DR809924.1|DR809924
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13125967|gb|BG316642.1|BG316642
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|94479916|gb|EB708874.1|EB708874
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13315903|gb|BG410251.1|BG410251
EST:     GGGCAAGGAGTATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGCACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGAT
genomic: GGGCAAGGAG-ATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGG-ACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGAT
EST: gi|110219228|gb|EC901126.1|EC901126
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATG                         CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTTTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATG

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: 31 (upstream exon), 45 (downstream exon)
Score: 9

GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 423

GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG


Block sizes: 34 (upstream exon), 38 (downstream exon)
Score: 8

GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG


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

GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgatta ... gtaattgcagCTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACTTGAAACCTGGCGCCGATGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAATGCAACAGTCATCATGgtatcgattattcagctcatcatccatatccctgcatgaaattgctagctatctgtttaatcaaccagtcgatcatgcagatatgcatgctatgcatgct

- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG