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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgatgtccatgggcatacctttgagaccaacttcgttttggtttttatgtgtttctttgcctgtcctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG

Basic information

species Zea mays
transcript GRMZM2G097421_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097421_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g35570.1 (Oryza sativa), 3'ss of exon 5
gtaaatgatgtccatgggc-------atacctttgagaccaacttcgttttggtttttatgtgtttctttgcctgtcctttg----gttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG
|||| |||| || |||| |       || ||||||     | ||| || | |  ||| ||  |||| |||  ||    ||||    | |||||||||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| | ||||||||||||||||
gtaagtgatctctatggactatgaaaatgcctttgttgttagcttggtctggtgtttaataggtttgtttatcttatttttgttatgctagGTAATGAGCATAAAGGCAGTTGGTATTGCAATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAAACTTGGTTATTTGCAACTGTTTCAG
















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|78118379|gb|DV536765.1|DV536765
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|149012854|gb|EE042696.2|EE042696
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|74236901|gb|DT644815.1|DT644815
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|149101364|gb|EE187481.2|EE187481
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|148951157|gb|EC896836.2|EC896836
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|40334623|gb|CK368693.1|CK368693
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|148947645|gb|EC893125.2|EC893125
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|74244190|gb|DT652104.1|DT652104
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|148942011|gb|EC887002.2|EC887002
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GGAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|71416856|gb|DR803834.1|DR803834
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAGGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|148972078|gb|EE022933.2|EE022933
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTAACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|149005298|gb|EE039847.2|EE039847
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|149070089|gb|EE158489.2|EE158489
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|91050129|gb|EB160547.1|EB160547
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|149013793|gb|EE043260.2|EE043260
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCTAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|148948891|gb|EC894305.2|EC894305
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|94477226|gb|EB706184.1|EB706184
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCCAGCTTACA-TTGAAGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|71446399|gb|DR827449.1|DR827449
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|76012865|gb|DT940035.1|DT940035
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
EST: gi|50323304|gb|CO518430.1|CO518430
EST:     CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACG                         GTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC
genomic: CAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGC

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), 49 (downstream exon)
Score: 133

GACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 185

GACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGGAATTTGCTCAGTGATAGGATCTTTGACGgtaaatgatg ... ctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagaccaacttcgttttggtttttatgtgtttctttgcctgtcctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG
                               tttctttgcctgtcct  CT-rich tract
                     tttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgatgtccatgggcatacctttgagaccaacttcgttttggtttttatgtgtttctttgcctgtcctttggttagGTAATGAGCATCAAGGCAGTAGGCATTGCTATCAAGCTTACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT