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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagattcattggcatcttgtttcaggctttctgtaatttcttcaagattatgtgaaaaattggaccgtgatgtagcatttgacatgaatggcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 2
gttaagattcattggcatcttgtttcaggctttctgtaatttcttcaagattatgtgaaaaattggaccgtgatgtagcat-ttgacatgaatggcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG
           |  |  | |  |     |   | |  ||||||||| |  |    || ||| ||| ||  || |||| ||| | ||  ||||||| ||||||||||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||
----------gtaagtctatcatgatgagaagttt--aatttcttccatgtgccatgtaaatttg-actttgttgtaacatgtcgaactgaatggtaaatccagGAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG
















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|13490381|gb|BG517145.1|BG517145
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|32827648|gb|CD967326.1|CD967326
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTA
EST: gi|67039601|gb|CO465856.1|CO465856
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     SCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     SCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|32827665|gb|CD967343.1|CD967343
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAAC
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAAC
EST: gi|211089520|gb|FL366816.1|FL366816
EST:     C-GAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|32827846|gb|CD967524.1|CD967524
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTA
EST: gi|32931957|gb|CF036769.1|CF036769
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAGGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|32933926|gb|CF038738.1|CF038738
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
EST: gi|211304793|gb|FL143342.1|FL143342
EST:     CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAG                         GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA
genomic: CCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATA

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: 3582

TGGTGTTGCCCCTTCTGGGTACAAGAACAGCAGCAGCACCAGCATTGGTGCCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1230

TGGTGTTGCCCCTTCTGGGTACAAGAACAGCAGCAGCACCAGCATTGGTGCCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1207

TGGTGTTGCCCCTTCTGGGTACAAGAACAGCAGCAGCACCAGCATTGGTGCCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1765

TGGTGTTGCCCCTTCTGGGTACAAGAACAGCAGCAGCACCAGCATTGGTGCCGAAAAGTTGCAAGATCACATGAACGAGCTAAAGATTAGAGATGATAAGgttaagattc ... gcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatgtgaaaaattggaccgtgatgtagcatttgacatgaatggcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG
                               atttgac  putative branch site (score: 1765)
       tgaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagattcattggcatcttgtttcaggctttctgtaatttcttcaagattatgtgaaaaattggaccgtgatgtagcatttgacatgaatggcaaatccagGAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA