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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgcaatttctcccttttcttcctgtcgggcggagatagtagtatattcttcgaggaaacctaggtgattgcaatgtcgttttgatgatgatgattcccgaccattttatctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 1
splice site 3'
intron type U2

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|211442448|gb|FL216159.1|FL216159
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|211013809|gb|FL029070.1|FL029070
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|71427181|gb|DR808231.1|DR808231
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|211013807|gb|FL029068.1|FL029068
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|78092884|gb|DV521258.1|DV521258
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|71427954|gb|DR809004.1|DR809004
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|30591321|gb|CD052314.1|CD052314
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|74235679|gb|DT643593.1|DT643593
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|26559396|gb|CA831631.1|CA831631
EST:     TCCATCATCCCAAGCTTTCTTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: TCCATCATCCCAAGC-TTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|50327717|gb|CO522843.1|CO522843
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|211013810|gb|FL029071.1|FL029071
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|71449152|gb|DR830202.1|DR830202
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|76291810|gb|DV031378.1|DV031378
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|50331812|gb|CO526938.1|CO526938
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|22542326|gb|BU092764.1|BU092764
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|50324082|gb|CO519208.1|CO519208
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|87156327|gb|DY401116.1|DY401116
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|211013808|gb|FL029069.1|FL029069
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|76289427|gb|DV028995.1|DV028995
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
EST: gi|211442449|gb|FL216160.1|FL216160
EST:     ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAA                         GGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT
genomic: ATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 51

GAGAACCGCCGCCGCACAACCCCGGACGTGGTGGCAGGCGACCGATCCGGATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

GAGAACCGCCGCCGCACAACCCCGGACGTGGTGGCAGGCGACCGATCCGGATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 18

GAGAACCGCCGCCGCACAACCCCGGACGTGGTGGCAGGCGACCGATCCGGATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 68

GAGAACCGCCGCCGCACAACCCCGGACGTGGTGGCAGGCGACCGATCCGGATCCATCATCCCAAGCTTCCTTTCTGTCTCCTCTTCATCCATCTCCACAAgtaagatgca ... atctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgattgcaatgtcgttttgatgatgatgattcccgaccattttatctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT
                ttttgat  putative branch site (score: 68)
                                         ttttatct  putative PPT
                                        attttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgcaatttctcccttttcttcctgtcgggcggagatagtagtatattcttcgaggaaacctaggtgattgcaatgtcgttttgatgatgatgattcccgaccattttatctgcacagGGATAATCAAGGAAGGAAGGCCATGGTTTTGTTCGAACTTGACCCGGACATCATCCGATGGGGTCTTCACCATCTCCTCCCCGCTCCGGCTGGATACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA