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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataacttgatgaaccttttcctgaccatgtaaggctggtttctcaaacactatgaactgagtatgtctcagtgagctttgttatatatgctgtttct...

Basic information

species Zea mays
transcript GRMZM2G115372_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115372_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g63500.2 (Oryza sativa), 5'ss of exon 11
AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataacttgatgaaccttttcctgaccatg-taaggctggtt-tctcaaacactatgaactg-agtatgtctcagtgagctttgttatatatgctgtttct-------------------------
|| | ||||| || |||||||| ||| |||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||||||  |  ||  |   |||  ||  |||| |    |  | | |||  || | |  | | |  || |  | | | |  ||    | ||  |   || || |                         
AGCTCTACAATCATCACTGCCGTCTTGTATGTCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGATGAAGGACCTCTTTTTGACTTGGAGAGgtaatatttgcatttatactttgttgtacatggtgcttccagctgtctgcaatatttcgcattacagaagtttttaatttgcaacataattcagagtgatttttgacatgggaggtcatgttatgcag

upper sequence: GRMZM2G115372_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv04s0008g05270.t01 (Vitis vinifera), 5'ss of exon 12
AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataacttgatg-----aaccttttcctgaccatgtaaggctggtttctcaaacactatgaactgagtatgtctcagtgagctttgttatatatgctgtttct
|| | ||||| || || ||| ||||  | ||    || || || || ||||||||||| || ||||||||||| || ||| | ||||||||||| |||||| ||  | |   |      | | | | |  |||       |  ||  ||||   |   | |  | |   | | | |   | |      |  |  |  || ||   
AGCTATACAATCATCATTGCTGCCTGTTCTGTTCTGCAGCTTCTTCTATTGATGATCTGTTCCAAGGAACTGAAGAGGGAACCCTTTTTGATTTGGAGAGgcaagtagtcattatcctcagcttgtgctcgacacctcctgattgtcttcttgtattttcttcagtttttttattt---ttaatcacatcttccagcctctta--
















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|149088177|gb|EE287320.2|EE287320
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32844278|gb|CD983959.1|CD983959
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|78076776|gb|DV505210.1|DV505210
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|166648248|gb|EG114153.1|EG114153
EST:     GACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
genomic: GACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32844832|gb|CD984513.1|CD984513
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32845460|gb|CD985141.1|CD985141
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32836721|gb|CD976399.1|CD976399
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32844915|gb|CD984596.1|CD984596
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|32844695|gb|CD984376.1|CD984376
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAACTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
EST: gi|83278407|gb|DV942415.1|DV942415
EST:     GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAG                         TTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT
genomic: GATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTT

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), 46 (downstream exon)
Score: 27

AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 30

AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 17

AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataactt ... tgctatgcagTTTTCAGTTTGAAACCGAGTCCGAAGGGACAAAGCTGAGGAGGGATGTTTTGGCGGAAGGCAATGCTGGCTCAGGACCATCTACTACCGGCCTTGTGGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTACAACCACCACTGCCGCCTTATATGCCTAGCTGCCTCATCCATTGATGATCTTTTTCAAGGAACTGAGGAAGGACCTCTTTTTGATTTAGAGAGgtaataacttgatgaaccttttcctgaccatgtaaggctggtttctcaaacactatgaactgagtatgtctcagtgagctttgttatatatgctgtttct

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