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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag

Basic information

species Zea mays
transcript GRMZM2G038195_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g12580.1 (Oryza sativa), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
||| ||||||||||| ||||| ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||   ||| | |  ||  |||| |  ||  ||||||||| |  |||||||    | | |||| |||  | || |||||| | ||
CTACGATGAATGCTTGAGAAAGTATGGAAATGCAAATGTATGGAAATACTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAACCAGgtttgttacttgactaattgcggttta-actgatataggcttatccaatatatg---cctgacatgtga--atcacccattttatag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G17100.1 (Glycine max), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||| || || || || || | |||||| ||  |  ||| |  |   |  || |  | | |     ||      |||    |||||||  ||  |      |  ||| ||   
CTATGATGAATGCTTGAGAAAATATGGAAATGCGAATGTCTGGAAATACTTTACAGACTTGTTTGATTATTTGCCTCTGACTGCCCTCATTGAGAGTCAGgtttgagt--taaatgttgcagagtggttatctgactaattt------tatgccggcctttaacttctacctctgtgtattgcag--

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G40490.1 (Glycine max), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || || || || || | |||||| || |  | ||| ||||   |   ||| |  | | | ||  ||   |||    || ||||  ||      | |            
CTATGATGAATGCTTGAGAAAATATGGAAATGCCAATGTCTGGAAATACTTTACAGACTTGTTTGATTATTTACCTCTGACTGCCCTCATTGAGAGTCAGgtttg-agttaaatatgttgcag--aatgttcatct-gactaattt--tatgccagcatttaacttctgtgtatacag---------

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G04570.1 (Glycine max), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
||| ||||||||||| ||||| ||||||||||| ||||| ||||| |  ||||| || |||||||||||||| ||||| || || ||||| || | |||||| || |  ||||| ||||   |   ||| | || | | ||   |       ||||||      | | | |  | |  || | ||||
CTACGATGAATGCTTGAGAAAGTATGGAAATGCCAATGTCTGGAAATTCTTTACCGATTTGTTTGATTATTTACCTCTGACCGCCCTTATTGAGAGTCAGgtttg-agtttaatatgttgcag--aatgtttttct-gactacct-------tatgcc--agtgtctaacatccttgtatattacag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G02990.1 (Glycine max), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatg-gttgatgctattataggcttgt-tgaatatata-tgcctttacatttgagaaacatccatttcacag
|||||| |||||||| ||||| ||||||||||| ||||| ||||| |  || || ||||||||||||||||| ||||| || || ||||| || | |||||| || |  | ||| ||||      || | || | |  | ||| |   | | | ||    | ||  || | | |                
CTATGACGAATGCTTGAGAAAGTATGGAAATGCCAATGTCTGGAAATTCTTCACCGACTTGTTTGATTATTTACCTCTGACTGCCCTTATTGAGAGTCAGgtttg-agttaaatatgttgcacaatgtttctttgactgccttatgccagtgtctaacatccttgtatgttacag---------------

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G59830.2 (Arabidopsis thaliana), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggc--ttgttgaatatatatgcctttacatttgagaaacatccatttcacag
 ||||| |||||||| || ||||| |||||||||||||| |||||||||||||| ||| | || |||||| | ||||| ||||| || ||||| | ||||||  | | ||    |||  |    | ||  ||| ||  |   |||||  |  |     | |||     | |     || |   | ||||
TTATGACGAATGCTTGAGGAAATACGGAAATGCAAATGTGTGGAAGTATTTTACGGACCTTTTCGATTATCTCCCTCTTACAGCACTCATAGAGAGTCAGgttcg-agctgttcttgccagtcgtcattgtatcatccgtagttgtttcacttccgcacttttcttcatcaactgtattc-cgtgacag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G69960.1 (Arabidopsis thaliana), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggc---ttgttgaatatatatgcc--tttacatttgag---aaacatccatttcacag---
 ||||||||||| || || |||||||||||||| |||||||||||| | || || ||  | ||||||||| | || || ||||||||||| || | ||||||||  |    || |  | |  |||    |||   ||| |    | ||   | | | |||   |||  | ||||    | |  ||  |||  | |   
TTATGATGAATGTTTGAGGAAATATGGAAATGCTAATGTATGGAAGCACTTCACTGATCTTTTTGATTATCTTCCACTTACAGCTCTTATTGAGAGTCAGgtatttaaaa-aactaatgagcgttttcactaccttagacaatctcttctctgtttctgctgttttggacttgactacagaactctttttttctgtag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G10430.1 (Arabidopsis thaliana), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattatagg-cttgttgaatatatatgcctttacatttgagaaacatccatttcacag
 ||||| |||||||| || || || |||||||| || || |||||||||||||||||| | || |||||| | ||||| || || || ||||| | ||||||  |     |  ||| | |  |||| || | | |||   ||| ||  |  || | || |||  | || |  ||     ||||   ||
TTATGACGAATGCTTGAGGAAGTACGGAAATGCTAACGTCTGGAAGTATTTTACAGACCTTTTCGATTATCTTCCTCTTACCGCCCTCATAGAGAGTCAGgttagagctgttctttctca--gttggtgtt-tgatacatctttttctaagtaca-gctttttgacttcatcaa-----attttgtag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0026g01080.t01 (Vitis vinifera), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatg---catcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
 ||||| |||||||| ||||||||||||||||| ||||| |||||||||||||| ||| | ||||||||| | || || ||||| || || || | |||||| ||     ||    ||| ||||| ||  | || | |||   ||  ||| |  |||     | |||       |   |  ||  || ||
TTATGACGAATGCTTGAGAAAATATGGAAATGCCAATGTCTGGAAGTATTTTACCGACCTTTTTGATTATCTACCCCTTACAGCCCTCATTGAGAGTCAGgtttgagttgtccatgtttcttatgttt--tactttgataaatttcctgactg-atac----tgacagccatatattgtttataccatag

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0066g02240.t01 (Vitis vinifera), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
 |||||||||||||||||||||||||||||||||||||| |||||  ||||||| ||  | ||||||||  | || |||||||| ||||| || | |||||| || ||||   ||  || ||  |  |  | |  | |  |   |  || | ||     |  ||     ||    |  || |     
TTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTCTGGAAACATTTTACTGATCTCTTTGATTACCTACCCCTCACAGCGCTTATTGAGAGTCAGgtctg-atctc--ttgattttgcgtatttttgtgtttgattcaatccatgt-taatttatgccaaccttgatttgtttatgtag---

upper sequence: GRMZM2G038195_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g05330.t01 (Vitis vinifera), 5'ss of exon 3
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgtta---tggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag
 |||||||||||||| ||||||||||| ||||||||||| ||||| ||||| || ||| | ||||||||| | ||||| ||||||||||| || |  ||||| || ||  ||   || |    |  ||| |    |||    ||| ||||  |  | |    |  | ||  ||                 
TTATGATGAATGCTTGAGAAAATATGGGAATGCAAATGTCTGGAAATATTTCACCGACCTTTTTGATTATCTACCTCTTACAGCTCTTATTGAGAGCCAGgtttgaattatataatgcttccttatttggtttccttaatatcttattgacaacctttattgtgtctttgtag-----------------

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|7238085|gb|AW573457.1|AW573457
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|28361586|gb|CB239942.1|CB239942
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|76019955|gb|DT947125.1|DT947125
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCCCAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|71767226|gb|DR965163.1|DR965163
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|28390354|gb|CB250174.1|CB250174
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|14245080|gb|BG873662.1|BG873662
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|76936424|gb|DV174722.1|DV174722
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|148967589|gb|EE018838.2|EE018838
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|211172730|gb|FL265205.1|FL265205
EST:     ACAGACTTTGTTTGATTATTTGCCTCTCACAGCTCATATAGAAAAATCAC                         GTCTTCTGTCTTCATGGAAGCGCTCTCTGCGTCATTGGACACATTGGGAT
genomic: ACAGACTT-GTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAA-TCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGC-CTCTCTCCGTCATTGGACACATTGG-AT
EST: gi|22472908|gb|BU037388.1|BU037388
EST:     TTACAGAC-TGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|78106567|gb|DV524985.1|DV524985
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|32932098|gb|CF036910.1|CF036910
EST:     TTACAGACTTGTTTGATTATTCGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|78106568|gb|DV524986.1|DV524986
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|76913645|gb|DV165204.1|DV165204
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
EST: gi|29167965|gb|CB411225.1|CB411225
EST:     TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAG                         GTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC
genomic: TTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAAC

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: 47 (upstream exon), 48 (downstream exon)
Score: 116

CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAACATTCGTTCTCTTGATCGCATACAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAACATTCGTTCTCTTGATCGCATACAGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 112

CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAACATTCGTTCTCTTGATCGCATACAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatct ... catttcacagGTCTTCTGTCTTCATGGAGGCCTCTCTCCGTCATTGGACACATTGGATAACATTCGTTCTCTTGATCGCATACAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGATGAATGCTTAAGAAAATATGGAAATGCAAATGTATGGAAGTATTTTACAGACTTGTTTGATTATTTGCCTCTCACAGCTCTTATAGAAAATCAGgtatgcatcttaatttgttatggttgatgctattataggcttgttgaatatatatgcctttacatttgagaaacatccatttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC