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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctgtacctctacttcactattcacctgtgtttgtcactacttagcggctattctgtcattctgagacggtctgagcaaaagttcactcctgtatttttgctataattagctctgcgttcttgtgaaatttcaatcgtatttgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC

Basic information

species Zea mays
transcript GRMZM2G409104_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 2
gtaagcctgtacctctacttcactattcacctgtgtttgtcactacttagcggctattctgtcattctgagacggtctgagcaaaagttcactcctgtatttttgctataattagctctgcgttcttgtgaaatttcaatcgtatttgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC
                                                            |||| |   |  ||||        | |||| ||   | |||  || |  ||||  |   |  ||||  ||||||  |   |||         |||||||||||||| |||||| ||||||||||||||||| ||||| |  || |  |||||  | || ||||||||| | | |||||| || || || |||||||
------------------------------------------------------------gtcagtagtacccggtt-------aggttcgct---gaattggtgttcgaattgaccgcgaattctgatgaaatcccccgcgt--------cgcagTTCGAGATGAGGGAGCCGAGGCTGTGCCAGATCGTCTGCAAAACCGCGCTGACCCATCAGGAGGCGAAGGATTTCAGGGAGAAGATCGACGACGAGTACC
















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|78110631|gb|DV529039.1|DV529039
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|148965278|gb|EE016081.2|EE016081
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|89250725|gb|DY622511.1|DY622511
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|101390012|gb|EB816938.1|EB816938
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|149013945|gb|EE043446.2|EE043446
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|149102922|gb|EE288273.2|EE288273
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|149096266|gb|EE181975.2|EE181975
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
EST: gi|91871094|gb|EB401239.1|EB401239
EST:     ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTG                         TTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA
genomic: ACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCA

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: 49 (upstream exon), 45 (downstream exon)
Score: 54

CTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCGTCGATAGCGCCGAGAACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 57

CTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCGTCGATAGCGCCGAGAACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

CTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCGTCGATAGCGCCGAGAACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 120

CTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCGTCGATAGCGCCGAGAACCTTGGCGAGGTGCTCCGCGGCGACCGCATCGAGAATTCACTCTACGTGgtaagcctgt ... tgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctataattagctctgcgttcttgtgaaatttcaatcgtatttgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC
                             aaatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctgtacctctacttcactattcacctgtgtttgtcactacttagcggctattctgtcattctgagacggtctgagcaaaagttcactcctgtatttttgctataattagctctgcgttcttgtgaaatttcaatcgtatttgaaatgcagTTCGAGATGATGGAGCCTAGGCTGTGCCAGATCGTGTGCAAGATTGCTCCAACCCAAGATGAAGCGAAGGATCTGAAGGAGAAAATTGAGGATGAGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG