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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggtgtactcttattttctttctcaggctgtatgctagttgaactattgtgctggtaaatttttataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 19
gtactggtgtactcttattttctttctcaggctgtatgctagttgaactattgtgctggtaaatttttataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG
             | | | | ||||||||     | || |       ||| | |  |  ||  ||| || |  || ||| | | ||||    ||                || | || ||||||| ||||| || || ||||||||||||||||| || ||| |||||||||||||||| || || ||||||||| |||| |||
----------gtacatgtgtactttctcatagcatttgttcccccttctaattttattttat-tttatacaatggaatgatatattctgactac---------------cctaccttgtacagCCTATTGTAAATGTTGAGGAGAAGTTTCATATATTATGCTCAAAAGATAGTGGGGTACTTTATGAGGATCCTCACATTCAG
















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|211363573|gb|FL059329.1|FL059329
EST:     TGGTGACTTGGCACTTGCTACCCTTGATGATCAGGTCCAACTCAGTTCAG                         CCAATTGTCAACGTTCCGAAGGAGAAGTTTTCATATTTTGTGCAC
genomic: TGGTGACTTGGCACTTGCTACCCTTGATGATCAG-TCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGT-C-GA-GGAGAAGTTT-CATATTTTGTGCAC
EST: gi|71439223|gb|DR820273.1|DR820273
EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
EST: gi|211363570|gb|FL059326.1|FL059326
EST:     TTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
EST: gi|40336758|gb|CK370828.1|CK370828
EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
EST: gi|38502665|gb|CF972525.1|CF972525
EST:     CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
genomic: CTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGT
EST: gi|211363572|gb|FL059328.1|FL059328
EST:     TGGTGACTTGGCACTTGCTACCCTTGATGATCAGGTCCAACTCAGTTCAG                         CCAATTGTCAACGTCCGAGGAGAAGTTTCATATTTTGTGCACAAA
genomic: TGGTGACTTGGCACTTGCTACCCTTGATGATCAG-TCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTC-GAGGAGAAGTTTCATATTTTGTGCACAAA

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), 49 (downstream exon)
Score: 97

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

TGCTGTAGAGCAAAATCCTGCCCAAGGATTGAATGCTAATCAAAGTCCAGCTGGTGACTTGGCACTTGCTACCCTTGATGATCAGTCCAACTCAGTTCAGgtactggtgt ... ctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG
                   tactgac  putative branch site (score: 84)
                                        ttctgcttt  putative PPT
                                 aaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggtgtactcttattttctttctcaggctgtatgctagttgaactattgtgctggtaaatttttataggggcatgttctcttctactgacacctgtgaaatgaattctgctttatacagCCAATTGTCAACGTCGAGGAGAAGTTTCATATTTTGTGCACAAAAGATAGTGGGGTGCTGTACGAGGATCCTTACATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT