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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctacatcaatgctctttgtttacaacattacatttagctgctcatcacctgtattgtattagggaaatcctcgtgttcgtaccttgcacaatgtt...

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 5'ss of exon 3
TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctacatcaatgctctttgtttacaacattaca------tttagctgctcatc---acctgtattgtattagggaaatcctcgtgttcgtaccttgcacaatgtt
||||||||| || ||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||||||  |||  |  |||||| | |   ||     ||||       ||   |  || |      |     |||||||||  |||  | |     | |   ||   |      
TGATGTGACAAAAAGTGGAGATGCACGTGTTGGTTTGGTGGGCTTTCCTTCAGTTGGAAAATCAACATTGTTGAACAAGCTGACAGGAACATTTTCAGAGgt--gctgtacgaatgctatctacatattcatttacgaggatcttcccccacttagttgagcaccctttgtattagataaacgcacacacacat-ttttatgc------

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 3
TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctac-------atcaatgct---ctttgtttacaacattacatttagctgctcatcacctgtattgtattagggaaatcctcgtgttcgtaccttgcacaatgtt
||||||||| || ||||||||| |  | |||||  | || || |||||||||||||| ||||| ||  | || |||||||| || ||||||||||| ||||||||           |  |||  |   |||  |||      ||  | || |    |    ||||     ||||    |  |||||  |  | ||  |||          
TGATGTGACTAAAAGTGGAGATTCTAGAGTTGGACTGGTCGGATTTCCTTCGGTTGGAAAATCTACGCTATTAAACAAGCTGACTGGGACATTTTCCGAGgtttgtagttatcgttacgaatattgaacttcctttctcttgttgtaattggaattttgaaacctaccacgtatccatggcatcctatttctagttactt----------
















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|32836870|gb|CD976548.1|CD976548
EST:     CGGTGGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211270941|gb|FL142975.1|FL142975
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211268510|gb|FL142969.1|FL142969
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACNACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|32837261|gb|CD976939.1|CD976939
EST:     GACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: GACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211268500|gb|FL142959.1|FL142959
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|71769273|gb|DR967210.1|DR967210
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|32919863|gb|CF024675.1|CF024675
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|32839263|gb|CD978944.1|CD978944
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|32848352|gb|CD988033.1|CD988033
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|67034867|gb|CO463400.1|CO463400
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|60353675|gb|DN220648.1|DN220648
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|74240038|gb|DT647952.1|DT647952
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211270940|gb|FL142974.1|FL142974
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|26559128|gb|CA831363.1|CA831363
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|71418217|gb|DR804368.1|DR804368
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|76937221|gb|DV175090.1|DV175090
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211268513|gb|FL142972.1|FL142972
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|71436936|gb|DR817986.1|DR817986
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211270942|gb|FL142976.1|FL142976
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTAC
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTAC
EST: gi|211268499|gb|FL142958.1|FL142958
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTAT
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTAT
EST: gi|30306602|gb|CD001275.1|CD001275
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|67042509|gb|CO468764.1|CO468764
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|33094247|gb|CF054241.1|CF054241
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211270943|gb|FL142977.1|FL142977
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|22520897|gb|BU079708.1|BU079708
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|22542275|gb|BU092713.1|BU092713
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|87155566|gb|DY400355.1|DY400355
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|71312952|gb|DR792998.1|DR792998
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|74233974|gb|DT641888.1|DT641888
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|60343127|gb|DN210100.1|DN210100
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|116817757|gb|EC860667.1|EC860667
EST:     CGGTTGGGAAATCAACATTGTAGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTATACAACTTTAACATGTATTCCTGAAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|6527040|gb|AW216258.1|AW216258
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|211268507|gb|FL142966.1|FL142966
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
EST: gi|32836350|gb|CD976028.1|CD976028
EST:     CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAG                         GTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG
genomic: CGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 245

TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATGTATAAGGGTGCTAAAATCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 156

TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATGTATAAGGGTGCTAAAATCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 153

TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATGTATAAGGGTGCTAAAATCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 179

TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctaca ... tgtttcaaagGTTGCTTCCTACGAGTTTACAACTTTAACATGTATTCCTGGAGTTATCATGTATAAGGGTGCTAAAATCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTGACGAAGAGTGGAGATGCACGTGTTGGTTTAGTTGGCTTTCCTTCGGTTGGGAAATCAACATTGTTGAACAAGCTAACAGGGACATTTTCAGAGgtttgctacatcaatgctctttgtttacaacattacatttagctgctcatcacctgtattgtattagggaaatcctcgtgttcgtaccttgcacaatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT