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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

Basic information

species Zea mays
transcript GRMZM2G155437_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 5
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaa--acttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                                                          ||  |  ||   ||||| |  |  | | || | || ||  |      || |||   ||  |  || ||  || || || ||||||| |||        || ||           ||   |||||| |||||||||||||||||  |||||||||| |||||||| ||||| || |||||||||||||||||||| ||||||||  |||||||||
---------------------------------------------------------gctgtggtgtctgcaatgcacaatatgtctggaataactatt------cactttctcttcttcataaaacatggtttactaaatttagaac--------atgat----------gatatgtcagGTGGAGCTTAAGGAAGGCCCCTTGGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGACTGCCAGTTCGTCTGAACAAAG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01430.2 (Oryza sativa), 3'ss of exon 4
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                                                       |  ||  |  ||   ||||| |   | | || | || ||  |      || | |   ||  |  || ||  || || || ||||||| |||||  |  |||                   |||||| |||||||||||||||||  | |||||||| |||||||| ||||| || |||||||||||||||||| | ||||||||  |||||||||
-------------------------------------------------------tagctgtggtgtctgcaatgcacaatgtctggaataactatt------cactctctcttcttcataaaacatggtttactaaatttagaacctgatgatatg------------------tcagGTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                  ||  || | |   || ||    | |||  | | ||  |   |   |  |  | ||  || |||   |    |    |  |  | |  | |||| | | |   | | | ||||||   |  ||||       ||  |||| |  |       || |  | ||||||| || |||||||| ||||| ||||||||||||||||||||||| ||| |||| || ||||  | | | || || ||  | |||||||
-----------------gtttgtgaacagaacttgtgccatctctatatactg--ttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatc-ttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0034g01000.t01 (Vitis vinifera), 3'ss of exon 5
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                                                                               | |    ||| |     | |    | |||    || | | ||| ||   | |||   |   ||  |   ||| ||  | |   |  |||  ||   |||||| |||||||| ||||| ||||| || |||||||||||||||||||| || || ||||||||||||||  | || ||||| ||||||||||
-------------------------------------------------------------------------------taaaacacagaaatctgtgatcatcttttcatattgcatatatgattcatctcatatatcctaacaaaatttcttgcattgaatccttaatatgtttcagGTGGAGCTTAAAGAAGGTCCTCTTGATCAGTTCACACATGAGATGGAACCCTTCCTACGCAAGCAAGGGATGCCGGTTCGGTTGAACAAAG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ38547 (Selaginella moellendorffii), 3'ss of exon 4
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttt-tataattttttttta-caattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                                                                                                                 | | |||| |   || ||   |   |        || ||  | ||  |   | | |   | | | ||||| || || || |||||||| ||||| || ||||| || ||||||||||||||||| || ||||||||| | || |||||  | |||| ||
----------------------------------------------------------------------------------------------------------------gtgcgtgtagacaatgcttttgcttttgcgtggttttcttcgtgtagctcactgtgagtgactacacagGTGGAACTCAACGAAGGCCCACTGGAGCAATTCACGCACGAGATGGAGCCATTTCTGCGAAAGCAAGGAATGCCTGTTCGTCTAAACAGAG

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|18450755|gb|BM429033.1|BM429033
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GNTGAGCTTAAGGAAGGCCCTCTGGAACAGNTCACACATGAGATGGAGCCC
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|211520197|gb|FL010166.1|FL010166
EST:     AATTTGAGGAGCATGATTT-GCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCC
genomic: A-TTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|211520200|gb|FL010169.1|FL010169
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCC-TCTG
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTG
EST: gi|32907095|gb|CF011908.1|CF011908
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCC
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|15100390|gb|BI396181.1|BI396181
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCC
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|211520196|gb|FL010165.1|FL010165
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACA
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACA
EST: gi|211009194|gb|FL302295.1|FL302295
EST:     ATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGGCAGATACG                         GTTKAGCTTAAGGAAGGCC-TCTGGAACAGTTCACACAT
genomic: ATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGG-CAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACAT
EST: gi|211520199|gb|FL010168.1|FL010168
EST:     ATTTGAGGAGCATGATTTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCC
genomic: ATTTGAGGAGCATGATTTT-GCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTT-AAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCC
EST: gi|211520198|gb|FL010167.1|FL010167
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCC-TCTGGAACAGTTCACACATGAGATGGAG
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAG
EST: gi|78081476|gb|DV509888.1|DV509888
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|78081475|gb|DV509887.1|DV509887
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
EST: gi|60394127|gb|DN226997.1|DN226997
EST:     AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG                         GTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA
genomic: AATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCA

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: 155

GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACGgtattctggt ... aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
                                               ttcctc  CT-rich tract
           aaatttacaacctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctggttttgctttttcatgtatatccctggtttggtttcttcaaattgactcactaggaagttgacaatgaaacttatttgcagtagctccttagtgccatttttggtttcttgtataatgtgtttcaccaaatttacaacctttttttataatttttttttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCATTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG