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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtcttcataccagtttttttgcacaacttctgccgttggtgtggtttttacattacgttcaccacttaacgactattaaataggactattgca...

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 6
GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtcttcataccagtttttttgcacaacttctgccgttggtgtggtttttaca---ttacg-ttcaccacttaacgactattaaataggactattgca
||||||||||| ||||||||| ||||||| || |||||||||||||| |||||||||||||| |||||||  ||  |||  ||  |    |    ||   |||  |    |   | ||    ||| |   ||||| || ||    |    |||  |||  | || |||    
GCTCATTACTACGAGGATGAGGCTGCTCCCACGGGCACATGTGCTGTCTGTGTTGTTGGTGGTGAAAGgtccgtcatctctattacc-cctcccggccttactggttatttgtatctgccacttataaacttacgatttacattatccttactcataaggaagattatg---

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 6
GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtcttcataccagtttttttgcac--aacttctgccgttgg--tgtggtttttacattacgttcaccacttaacgactattaaataggactattgca-
| ||| ||   ||||||||||||||| || ||||| |||||||| || || |||||||||||||| ||||  |||     |  || | |||    | |   ||  ||   |  ||   ||| |  || | ||  | | ||  |||  || | | |||  ||    | ||| | 
GTTCACTATCGTGAGGATGAGACTGCACCAACTGGTACATGTGCAGTTTGCGTTGTTGGTGGCGAGAGgtgagttcctaacccacaaatttggaagaatgtaatatccatcagtgagatgtagaattcaaatagc-tacaatactccaccaat-ttattta---tttttggaa

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 5'ss of exon 6
GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtcttcataccagtttttttgcac--aacttctgccgttgg--tgtggtttttacattacgttcaccacttaacgactattaaataggactattgca-
| ||| ||   ||||||||||||||| || ||||| |||||||| || || |||||||||||||| ||||  |||     |  || | |||    | |   ||  ||   |  ||   ||| |  || | ||  | | ||  |||  || | | ||   |     | ||| | 
GTTCACTATCGTGAGGATGAGACTGCACCAACTGGTACATGTGCAGTTTGCGTTGTTGGTGGCGAGAGgtgagttcctaacccacaaatttggaagaatgtaatatccatcagtgagatgtagaattcaaatagc-tacaatactccaccaatttttttt----tttttggaa

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|211433554|gb|FL254730.1|FL254730
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCNGCAAACTGGTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211433558|gb|FL254734.1|FL254734
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211430963|gb|FL254725.1|FL254725
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211535004|gb|FL000873.1|FL000873
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|87155643|gb|DY400432.1|DY400432
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAGAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211535005|gb|FL000874.1|FL000874
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211430956|gb|FL254718.1|FL254718
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211433550|gb|FL254726.1|FL254726
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGATGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211430955|gb|FL254717.1|FL254717
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|26559465|gb|CA831700.1|CA831700
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAGAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|32916313|gb|CF021125.1|CF021125
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGTGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|22546548|gb|BU098859.1|BU098859
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAGAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211433557|gb|FL254733.1|FL254733
EST:     AGACTGCTCCTACTGGCACATGTGCNTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCTTCC
genomic: AGACTGCTCCTACTGGCACATGTGC-TGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATC-
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|60395531|gb|DN228401.1|DN228401
EST:     GTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
EST: gi|211538002|gb|FL000876.1|FL000876
EST:     GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAG                         GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT
genomic: GAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCT

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), 48 (downstream exon)
Score: 153

GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 122

GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtc ... ctgtaaccagGTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCATTACTATGAGGATGAGACTGCTCCTACTGGCACATGTGCTGTATGTGTTGTTGGTGGCGAAAGgtttgttgtcttcataccagtttttttgcacaacttctgccgttggtgtggtttttacattacgttcaccacttaacgactattaaataggactattgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG