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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcag

Basic information

species Zea mays
transcript GRMZM2G006130_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgc-cttttgaaacatcactagatgcacttattttgaaagctgctgccgg-tgttgatgttcaaggttttggagctggatttttacttcag
|| ||||||||||||||||||||||| |||||||| || ||||| ||||||||||||||  ||  ||||||| ||| |    |   |  ||      |  |    | ||  ||      ||  |||| | || ||   |||   ||  | ||                     
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg------------------

upper sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 3
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttg-atgttcaaggttt---tggagctggatttttacttcag-
|| |||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||  ||| |||| |||               ||| || ||      |||||||||||||||  | |  | | | |     ||  |     | |   ||||  || ||   | |||| | 
GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcagttatttttg---------------ttgtaatat------atgcacttattttgatcgatcttccagataaaacataatttgcttctgaatggacatgaataaattcttctgc

upper sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 2
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcag
|||||||||||||| || ||||||||  | |||||||||||||| |  |||||||||     |  |    |  ||||          ||| |||    |  | |||||   |     |||  |          |   | ||     |||  |  ||               
GAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAGgtcattaatttccattacaatttctctaaaacttttaaatgataaaaaatgcaaacac----aaaaatatgtttcacataattcttttgaatttatgtactaat------------

upper sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 4
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgt-accccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcag
||||||||||||||||||||||||||  | ||||||||||||||||| ||||||||| |   |      |||||  ||| |    |      ||| | |   | ||  | |  ||||| |  | ||      | |   | | || |    | || || ||            
GAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAGgtcatttctaaatctcttgttttcagataacaaggacaaaaacccgaatatttaatgtttttgtattcagc-----atttctgtatgcatgagaatagaactaga------------

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|148950545|gb|EC896122.2|EC896122
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211169041|gb|FL129153.1|FL129153
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATTGACCCGTGGNCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|8367215|gb|BE050160.1|BE050160
EST:     GGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCCGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: GGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|88755664|gb|DY539805.1|DY539805
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211170726|gb|FL129169.1|FL129169
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211170714|gb|FL129157.1|FL129157
EST:     CAACCATGCANGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32844992|gb|CD984673.1|CD984673
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|148953656|gb|EC899016.2|EC899016
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32929289|gb|CF034101.1|CF034101
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211170722|gb|FL129165.1|FL129165
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|149082080|gb|EE171257.2|EE171257
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211169040|gb|FL129152.1|FL129152
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|148953586|gb|EC898940.2|EC898940
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|32844324|gb|CD984005.1|CD984005
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211170721|gb|FL129164.1|FL129164
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAATACATTGACCCGTGGTCC
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAA-ACATCGACCCGTGGTCC
EST: gi|91051534|gb|EB161952.1|EB161952
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|148956552|gb|EC902392.2|EC902392
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|149079201|gb|EE168160.2|EE168160
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCC
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCC-
EST: gi|211170720|gb|FL129163.1|FL129163
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|149100793|gb|EE186887.2|EE186887
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|60399112|gb|DN231926.1|DN231926
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
EST: gi|211169043|gb|FL129155.1|FL129155
EST:     CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG                         GTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCA

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: 48 (upstream exon), 47 (downstream exon)
Score: 221

GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 369

GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagc ... tttacttcagGTTTCGAAGCTGGAGGCTCTCATACTCCATCAAACATCGACCCGTGGTCCATCATTGGAGATGACTCCTCCGTGTTCGTGGCGACTGATCGTACATCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgccttttgaaacatcactagatgcacttattttgaaagctgctgccggtgttgatgttcaaggttttggagctggatttttacttcag

- - - - - - -  GGAGCT
- - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - GAGCTT