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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaatgtcatgttgtacattacatgacagaaatacacatcattagccctgtgcgccagttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccag

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 10
ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaatgtcatgttgtacattacatgacagaaatacacatca-ttagccctgtg-cgcc-agttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccag
                |||||| | |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||||||||||             || |||  |||   ||| |||| || | ||||   | || | |  ||||| ||   ||    ||  ||| |  |  |||  |||   |||| ||  |   |||| ||||
----------------GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCTgtaagta------------tatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacat--tcatttcataaatattttctgt-tacctttgaccag
















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|20337055|gb|BQ172685.1|BQ172685
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|33092593|gb|CF052587.1|CF052587
EST:     GTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: GTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|30087357|gb|CB885563.1|CB885563
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32865480|gb|CF005162.1|CF005162
EST:     AGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: AGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|60395660|gb|DN228530.1|DN228530
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|18172726|gb|BM348114.1|BM348114
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32928745|gb|CF033557.1|CF033557
EST:     ACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|60348494|gb|DN215467.1|DN215467
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|78544269|gb|DV621767.1|DV621767
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32916889|gb|CF021701.1|CF021701
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|16379449|gb|BI992951.1|BI992951
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|5740140|gb|AI947830.1|AI947830
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATTTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|32865498|gb|CF005180.1|CF005180
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|18170275|gb|BM340115.1|BM340115
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
EST: gi|23357521|gb|BU645170.1|BU645170
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         GTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACT

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: 408

ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaat ... ttttgtccagGTGGAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTTATCTTTCAGGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgaatgtcatgttgtacattacatgacagaaatacacatcattagccctgtgcgccagttcttgcattacccctgtcgacttcatggttttctaacatttttatgaatctttttgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG