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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttcttccccttaatttatgtgatctgccggttcaaggtttctcaaccttgtccgttccaagtttttggaccttataatgatagtttgtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG

Basic information

species Zea mays
transcript GRMZM2G527387_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g32490.1 (Oryza sativa), 3'ss of exon 14
cattttcttccccttaattta--tgtgatctgccggt-tcaaggtttctcaaccttgtccgttccaagtttttggaccttataatgatagtttgtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG
    || |    |   || ||  | | |  ||    | ||||   ||  ||| |   | ||       |||||    || | |  || | ||||||| ||||||| || || ||||| ||  |||| || ||||||||||| |||||||| || |||||   ||||||||||||||||||||||||||| |||||||||||  
-tccttatatttcaagatctagctctaacttgtttttatcaaaagttaccaatccatttcgaggtttttttttaattctgaca--gaaaatttgtctgctcagGATTCAATCGGGAGAATTGTATGTGTTCCATTGAAGCGTGCAAATGACATTATAGGGCAAACTACTGAAGAAATGGTGATGCGAGCTCAACAAGCTTCAA
















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|211103863|gb|FL454843.1|FL454843
EST:     ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGG                         GACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
genomic: ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
EST: gi|211103865|gb|FL454845.1|FL454845
EST:     ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGG                         GACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
genomic: ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
EST: gi|78105908|gb|DV524326.1|DV524326
EST:     ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGG                         GACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
genomic: ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
EST: gi|45568220|gb|CK985961.1|CK985961
EST:     ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGG                         GACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC
genomic: ATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATC

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: 29 (upstream exon), 43 (downstream exon)
Score: 4

ACGTTGCGAACAGCTCATCAAGGAAGAGTTTGGTATGGAGTGCAATTTTGATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 9

ACGTTGCGAACAGCTCATCAAGGAAGAGTTTGGTATGGAGTGCAATTTTGATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG


Block sizes: 41 (upstream exon), 14 (downstream exon)
Score: 3

ACGTTGCGAACAGCTCATCAAGGAAGAGTTTGGTATGGAGTGCAATTTTGATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 50

ACGTTGCGAACAGCTCATCAAGGAAGAGTTTGGTATGGAGTGCAATTTTGATGTTGTAGATGCTGTAAAGAAGCTAGAGAAACTCGGCATTGTTTCTCGGgtaagttaca ... gtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaccttgtccgttccaagtttttggaccttataatgatagtttgtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG
                                          tttgtct  CT-rich tract
                              ttataatgatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttcttccccttaatttatgtgatctgccggttcaaggtttctcaaccttgtccgttccaagtttttggaccttataatgatagtttgtctactcagGACTCGATTGGGAGGATCCTATGCGTCCCATTGAAGCGCGCAAATGAGATCATAGGAACAACTACTGAAGAAATGGTGATGCGAGCCCAACAAGCTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - tctgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttttg