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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgattaaatgggaagtgattcaaggtgaaatgttgtcaatagtattttgtgcacaacagaattttagtgaacaacattttataatccatgacgt...

Basic information

species Zea mays
transcript GRMZM2G071620_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071620_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 5'ss of exon 4
GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactga--ttaaatgggaagtgattcaaggtgaaatgttgtcaatagtattttgtgcacaacagaattttagtgaacaacattttataatccatgacgt----
||| ||||| ||||| ||  | ||||||||     ||| ||||||||| ||||||||||||||||||| ||  |||||||||||||| ||||||||||||||||| | |  |   | || || |  ||||||   |||| |      ||||||  | | |  |  | ||||||        |    | |   | |   |  |    
GAACCTTCTAGGTGAGGATTTAGCTCCACTGGCTACAAATGAACTTGAGCAGCTTGAGAGTCAAGTAGTCAGAACCTTGAAGCAAATCAGATCAAGAAAGgtaaattaacatagcaaggaaactcgttcaagtataaatat-----gtagtatact-taccgattaaaattttcagatttcatccgtaacgttgcgctagcttctt
















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|78085638|gb|DV514031.1|DV514031
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|78104752|gb|DV523170.1|DV523170
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|78104753|gb|DV523171.1|DV523171
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTANAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|211236050|gb|FL156597.1|FL156597
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|30031660|gb|CB833511.1|CB833511
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|50326015|gb|CO521141.1|CO521141
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|71448410|gb|DR829460.1|DR829460
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|18174972|gb|BM350360.1|BM350360
EST:     ATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: ATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|71762711|gb|DR960648.1|DR960648
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|50326014|gb|CO521140.1|CO521140
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|32165114|gb|CD670432.1|CD670432
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|50325855|gb|CO520981.1|CO520981
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|76285216|gb|DV024784.1|DV024784
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTANAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
EST: gi|32836421|gb|CD976099.1|CD976099
EST:     AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAG                         ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG
genomic: AGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 77

GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 24

GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgat ... catttggcagACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCTTCTTGGTGAAGAACTGGCTCCACTTAGCCCAAGTGAACTTGACCAGCTTGAGAGTCAAGTAGACAAGACCTTGAAGCAAATAAGATCAAGAAAGgtaaactgattaaatgggaagtgattcaaggtgaaatgttgtcaatagtattttgtgcacaacagaattttagtgaacaacattttataatccatgacgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaaca