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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaaatgttatagcatttaccttgtggtttttgtacatcactgaatgttcagctgcaagttgaaaaatttttaatcctctattttattgtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT

Basic information

species Zea mays
transcript GRMZM2G130548_T01
intron # 1
splice site 3'
intron type U2

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|211070403|gb|FL012978.1|FL012978
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|89755506|gb|DY685902.1|DY685902
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211067663|gb|FL012963.1|FL012963
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211070406|gb|FL012981.1|FL012981
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|32793956|gb|CD946192.1|CD946192
EST:     GATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCTGTA
genomic: GATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCTGTA
EST: gi|211064940|gb|FL012961.1|FL012961
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211070408|gb|FL012983.1|FL012983
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211067666|gb|FL012966.1|FL012966
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211070404|gb|FL012979.1|FL012979
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211067675|gb|FL012975.1|FL012975
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCC
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCC
EST: gi|211067676|gb|FL012976.1|FL012976
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
EST: gi|211067664|gb|FL012964.1|FL012964
EST:     TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGG                         GCCTTTGGTTTCACTTGCGTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT

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), 38 (downstream exon)
Score: 635

TCTACAGATTTCGCAGTTTTGCTGGGGGTAACTACGGAATGGGGGGCGGATCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT


Block sizes: 49 (upstream exon), 27 (downstream exon)
Score: 215

TCTACAGATTTCGCAGTTTTGCTGGGGGTAACTACGGAATGGGGGGCGGATCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 135

TCTACAGATTTCGCAGTTTTGCTGGGGGTAACTACGGAATGGGGGGCGGATCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 338

TCTACAGATTTCGCAGTTTTGCTGGGGGTAACTACGGAATGGGGGGCGGATCCGGATCTTTCCTCAAGGTCTTGGTCAACAACATGGATGTCCTCGCGGGgtacgcattc ... gtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttcagctgcaagttgaaaaatttttaatcctctattttattgtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT
                         ttttaat  putative branch site (score: 338)
                ttgaaaaatttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctaaatgttatagcatttaccttgtggtttttgtacatcactgaatgttcagctgcaagttgaaaaatttttaatcctctattttattgtcactgcagGCCTTTGGTTTCACTTGCGTATCCTCT

tgctaaa
- - - - - - - - - - -ccttgtg
- - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - ctgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - -cagctgc