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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgacttgactggatttctgtgatttgtgaccaaataaatag

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 5'ss of exon 9
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgact--tgactggatttctgtgatttgtgaccaaataaatag
 |||||| ||||||||||||||||||||||||||||||||  | | |||||||| |||||||||||||| |||||||||||||||||||||||||||||||||| |||  ||  |||| |||| |   |   | |  ||||   | |||       ||  ||   ||   ||  |     | || |    |   ||| ||
CTCACGGATAGCAGAGAAATTGGCTGCTGATTTGAAAGGCAAAATCAAATTGGAAGATGCTGGTTTTGACTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctgaagtcat--ttctgttcagttcttcgta-ttgtatataaaaaattcagtgcgtagctaccgagctgacctgacatacttttccatacccaaacag

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G01290.1 (Glycine max), 5'ss of exon 9
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgacttgactggatttctgtgatttgtgaccaaataaatag
|||| | || |||||||| ||||||| ||||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || || || ||||| |   |||| |    | ||  || | |  |    |||||     ||   | |   ||||   | | |  |   |    |   ||   |||    ||         
TTCAAGAGTGGCAGAGAAGTTGGCTGTTGATTTGAAGGGCCGCGTTAAATTGGAAGATGCTGGATTTGACTGGAAAATACTGGGCCCTGATGTCCTTCAGgtttcttacaat-cttttgtggataccataaaggcactaattcaattttcagttctataa--tagtttctctatggtatcttggtttcag--------

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G01300.1 (Glycine max), 5'ss of exon 10
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgactt----gactggatttctgtgatttgt-gaccaaataaatag
|||| | || ||||| |||||||||| |||||||||||| || |||||||| || |||||||| ||||| |||||||| || || || ||||| ||  |||| |    | | |||| | |    ||||||    ||||| |  |||   |  |||| | | ||     || |  ||||| || ||| | |        |  ||
TTCAAGAGTGGCAGATAAATTGGCTGTTGATTTGAAAGGTCGCGTTAAATTAGAAGATGCTGGATTTGACTGGAAAATACTGGGCCCTGATGTCCATCAGgttttttacaacattttttt---gtggata----tcataaaggcactgactcaattttcagttctataacagtttttctatggtttcttggtttcgggatcag

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G10610.1 (Glycine max), 5'ss of exon 10
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgac---ttgactggatttctgtgatttgtgaccaaataaatag
|||| | || |||||||| ||||||| ||||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || || || ||||| ||  |||| |    | || ||| | |  |    |||||     ||   | |   ||||   |   |    ||  ||    ||   || |||  |             
TTCAAGAGTGGCAGAGAAGTTGGCTGTTGATTTGAAGGGCCGTGTTAAATTGGAAGATGCTGGATTTGACTGGAAAATACTGGGCCCTGATGTGCATCAGgtttcttacaat-tttttgtggataccataaaggcactagttcaattttcagttctacaatagtttctctatggtttcttggtttcag-------------

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 10
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtcta--------aagctatatttctattcaatgga---taaaaatcatataaccaca-atcagaattgtga----cttgactggatttctgtgatttgtgaccaaataaatag
|||  | || ||||| || || |||| |||  | || || ||  |||||||||| ||||| || ||||| ||||||||||| || ||||||||||||||||| |         ||  |||   |||| |  ||| |   |   |  ||||||  | || ||   || ||| |    ||||    |   |      |||||     ||| |  ||
TTCCAGAGTGGCAGATAAGTTAGCTGTTGACCTAAAGGGTCGGATTAAATTGGAAGATGCAGGATTTGACTGGAAAATTCTGGGACCAGATGTTCAAGAGgtttcttaaatacaatttatgactctagttcatgcagtttcccatccatatattctcacattctaactgtaaatcccttgttgagtcatacccattttgttcttgaatga-cag

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: EFJ08918 (Selaginella moellendorffii), 5'ss of exon 9
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgacttgactggatttctgtgatttgtgaccaaataaatag
 || ||||||||||| ||  |||||   ||||||||||| ||| | ||| |||| ||||| |||||||| |||||||| ||||| ||||||||  | |||||      ||   ||||||            | ||| | || |  |  |        ||||  || | || || ||                      
CTCTCGGGTAGCAGAAAAGCTGGCTTTGGATTTGAAAGGTCGAATCAAACTGGAAGATGCGGGTTTTGACTGGAAAATACTTGGGCCAGATGTCAACGAGgt----gactg-gtttcta------------agatcttttagctgctttggt-----tgac--gagtagacttttgcag-------------------

upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 9
lower sequence: EFJ29772 (Selaginella moellendorffii), 5'ss of exon 9
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagcta-tatttctattcaatggataaaaatcatataaccacaatcagaattgtgacttgactggatttctgtgatttgtgaccaaataaatag
 || ||||||||||| ||  |||||   ||||||||||| ||| | ||| |||| ||||| |||||||| |||||||| ||||| ||||||||  | |||||     | |  ||      || |   | |     | |      |||  |   |                                             
CTCTCGGGTAGCAGAAAAGCTGGCTTTGGATTTGAAAGGTCGAATCAAACTGGAAGATGCGGGTTTTGACTGGAAAATCCTTGGGCCAGATGTCAACGAGgtgactggtttctaagatcttttagctgctgtggttgacgagtacacttttgcag--------------------------------------------

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|211226663|gb|FL216925.1|FL216925
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|211228708|gb|FL216926.1|FL216926
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|67019711|gb|CO448460.1|CO448460
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|67040057|gb|CO466312.1|CO466312
EST:     GAGGATGCTGGTTTTGATTGGAAAAT-CTTGGGTC-AGAATGTTCA-GAG                         GT-GATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGC
genomic: GAGGATGCTGGTTTTGATTGGAAAATTCTTGG-TCCAGA-TGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGC
EST: gi|33101148|gb|CF061108.1|CF061108
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|67026280|gb|CO455029.1|CO455029
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|67024223|gb|CO452972.1|CO452972
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|211228710|gb|FL216928.1|FL216928
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|24773212|gb|CA408466.1|CA408466
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|32846970|gb|CD986651.1|CD986651
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
EST: gi|211228712|gb|FL216930.1|FL216930
EST:     TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAG                         GTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT
genomic: TGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGT

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: 213

TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagct ... aaataaatagGTTGATTATGTTGCATGGGTTTGCGATCAGGATGCTTATGCTTGTAGCGGTCAGAAATGCTCTGCTCAGTCTGTTCTATTCATGCACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACGGGTAGCAGAGAAATTGGCTGCTGATTTGAAAGGCCGAGTTAAATTGGAGGATGCTGGTTTTGATTGGAAAATTCTTGGTCCAGATGTTCAAGAGgtctaaagctatatttctattcaatggataaaaatcatataaccacaatcagaattgtgacttgactggatttctgtgatttgtgaccaaataaatag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG