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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatacaaaccctattacacatatattcgcttcgcttcgatccgattcccctctctcctttttgttagccactaatccttcgtacgtgtgattcga...

Basic information

species Zea mays
transcript GRMZM2G087095_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087095_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatacaaaccctattacacatat-attcgcttcgcttcgatccgattcccctctctcctttttgttagccactaatccttcgtacgtgtgattcga-
|||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||| |  ||   |||| | || ||| | |    | ||   |    |  ||     ||||||   ||  ||| ||   | |||  |  ||  |  ||| |  
TCAAGAAGGCCTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCCCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCCTCCTCATCCAAgtaaacccactgcccctctcactcatctcagcttcctcctcttcccctaatcaaattctctcaacttgcttaacctgcactccc-caaac-cgcaatttgct

upper sequence: GRMZM2G087095_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0010g03900.t01 (Vitis vinifera), 5'ss of exon 1
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatacaaaccctattacacatatattcgcttcgcttcgatccgattcccctctctcctttttgttagccactaatccttcgtacgtgtgattcga----
|||||||||||||||| || ||  | ||||||||||||||||| || ||| || |||||||| |    ||    |||||| ||||||       ||| | ||||  | |||      |  | |  || |    | |   || ||| | |   |   || | | |      |  ||| || |    | |   |  |||       
TCAAGAAGGCGTACGAACTTTCGGTGCTCTGCGACGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTCTACGAGTTCTGCAGTAGCTCGAGgtaataacacaggaaa-agaaaaagtagaaa-acctaaatttgatacaaa--cttgcttttcataacacaaaacacaaagcaagagaaaaggaaattgttctct
















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|71315310|gb|DR794267.1|DR794267
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|6695990|gb|AW289098.1|AW289098
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCAGGTACCAGAGGTACATCTATGCTTCAGCCG
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGC-GGTACCAGAGGTACATCTATGCTTCAGCCG
EST: gi|50331176|gb|CO526302.1|CO526302
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|74236437|gb|DT644351.1|DT644351
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|78112771|gb|DV531165.1|DV531165
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|91870871|gb|EB401123.1|EB401123
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|8368837|gb|BE051782.1|BE051782
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|71330056|gb|DR801767.1|DR801767
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
EST: gi|211463199|gb|FL126648.1|FL126648
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 37

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatac ... ttaatatcagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGTACATCTATGCTTCAGCCGATGCTGCAGTGCCATCTAGCGATCAGATGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCAAgtaaccatacaaaccctattacacatatattcgcttcgcttcgatccgattcccctctctcctttttgttagccactaatccttcgtacgtgtgattcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctctc