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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgttctcttgttgtaatctttatattttttgttagtgtttcttaacgatccaagataatgacagctgtcggcgtgataccctattttgtacc...

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 13
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgttctcttgttgt-aatctttatattttttgttagtgtttct--taacgatccaagataatgacagctgtcggcgtgataccctattttgtacc
|||||||||||| || |||||||||||||||||||| |||||||||||  |||||   ||||| | ||| || || ||| ||||||||||| ||   |  | |  ||  |     | | |  | ||  | | |   ||  |     
TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattgtttctttgttttcaatgttgatttttcttgttagtgttgctaacattgttttaacctgccaccggatcactgctggctgctgcatcatcc---

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 13
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgt-tctcttgttgtaat-ctttatattttttgttagtgtttct--taacgatccaa----gataatgacagctgtcggcgtgataccctattttgtacc
|||||||||||| || || ||||||||||||||||| ||||||||||| ||||| | ||| |||  ||| |  | | ||| |||||||  || |   ||  | |  ||    |  ||||     | || |  || |||   ||        
TGATCATGAAGGTGGAAACGTCAGTGCTCATACTGGACATCTGgtaatttttgtatttctggtttcaatgcagtttttttcttgttagcattgccactattgttgtaaacctgccaatggatcatttctggctgctacatcat--------

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 13
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgta-atatttgttctcttgttgtaatctttatattttt----tgttagtgtttcttaacgatccaa--gataatgacagctgtcggcgtgataccctattttgtacc
|||||||||||| || ||||| |||||||| |||||||| ||||||  ||| |  ||||    ||| |  |||| |   ||    |    |   ||  ||| | | |    | |||  |    |||    ||                  
TGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTGgtatgtatatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttcatgtag----------------

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 13
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaa-tatttgttctcttgttgtaatct-ttatattttt-tgt-tagtgtttcttaacgatccaagataatgacagc-tgtcggcgtgataccctattttgtacc-------------------------------------------------------------------------------------------
|||||||||||||||||||||||||||||| ||||||||||| |||| |     |    | ||| ||||   ||| ||     ||| || | ||  |  |    | | | ||| | ||   | |   | |||     | |  || |                                                                                             
TGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTAgtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagaggaatgttctctattgactgatattatgctcaattcag

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|78179069|gb|DV549442.1|DV549442
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|31364242|gb|CD448597.1|CD448597
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GNTGGGAGTGCTCTGTCAGATCCTTTATCTT-CTTTCGCAGCGGCTCTTAA
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTT-ATCTTTCTTTCGCAGCGGCTCTAAA
EST: gi|116825307|gb|EC869024.1|EC869024
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT

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: 43 (upstream exon), 47 (downstream exon)
Score: 136

TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 581

TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 668

TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 413

TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttg ... ccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttgttctcttgttgtaatctttatattttttgttagtgtttcttaacgatccaagataatgacagctgtcggcgtgataccctattttgtacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagataa