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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcacgtgcacttcttatttcttgttcgaagatttgaattatttagtgctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG

Basic information

species Zea mays
transcript GRMZM2G165195_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------------------gtaatcacgtgcacttcttatttcttgt-tcgaagatttgaattatttagtg--ctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG
                                                                                          || |    |  |   | ||  |  |||| |  ||      || |  | | ||  |      ||  ||||  || |   || ||   ||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaact--cactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG

upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaatcacgtgcacttcttatttcttgttcgaagat-ttgaattatttagtgctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG
         || ||  |     ||  |        | | || |   || ||| |  |  |       |    ||||||  ||    | |      |  ||||||| ||||| || ||||| ||||| || || |||||  ||||  |||| ||||||||||| || ||||| || ||||| || |||||||||||  |  
gtgaaatatgtcattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
















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|211495219|gb|FL000399.1|FL000399
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|76010550|gb|DT937720.1|DT937720
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|91052905|gb|EB163323.1|EB163323
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|91054729|gb|EB165147.1|EB165147
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|211298305|gb|FL473376.1|FL473376
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|148991100|gb|EE032548.2|EE032548
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|71765371|gb|DR963308.1|DR963308
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|211512472|gb|FL332432.1|FL332432
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|32867970|gb|CF007652.1|CF007652
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|211493851|gb|FL175583.1|FL175583
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|71765372|gb|DR963309.1|DR963309
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|211490965|gb|FL175567.1|FL175567
EST:     CTCCAGAGTTGGCTAC-ACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGA
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGA
EST: gi|78074982|gb|DV503416.1|DV503416
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|21331789|gb|BQ487170.1|BQ487170
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|76281952|gb|DV021520.1|DV021520
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|32867969|gb|CF007651.1|CF007651
EST:     CTCCAGAGTTGGCTACCCCGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|76010551|gb|DT937721.1|DT937721
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|211095886|gb|FL432128.1|FL432128
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGMCCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
EST: gi|76933730|gb|DV173563.1|DV173563
EST:     CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAG                         GCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC
genomic: CTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGAC

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), 49 (downstream exon)
Score: 158

TCTGTCCAAAAGCACTGAAGTGATGAAAATTGTTAACAATCTAATGAAAGCTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TCTGTCCAAAAGCACTGAAGTGATGAAAATTGTTAACAATCTAATGAAAGCTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

TCTGTCCAAAAGCACTGAAGTGATGAAAATTGTTAACAATCTAATGAAAGCTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TCTGTCCAAAAGCACTGAAGTGATGAAAATTGTTAACAATCTAATGAAAGCTCCAGAGTTGGCTACCACGATGCAAGAATTTAGCAAAGAAATGACCAAGgtaatcacgt ... cttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaattatttagtgctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG
                                           ttcttactct  CT-rich tract
                          aaactaacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcacgtgcacttcttatttcttgttcgaagatttgaattatttagtgctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG