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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgatttcaactgtgttgcttctgcaccattttatgttcctgttattggagtatgatggaagtacttttacacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT

Basic information

species Zea mays
transcript GRMZM2G091563_T01
intron # 2
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|60337054|gb|DN204027.1|DN204027
EST:     CAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: CAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32920213|gb|CF025025.1|CF025025
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32921737|gb|CF026549.1|CF026549
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGCGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32920952|gb|CF025764.1|CF025764
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32826457|gb|CD966135.1|CD966135
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32922064|gb|CF026876.1|CF026876
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|60355748|gb|DN222721.1|DN222721
EST:     ACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: ACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
EST: gi|32920826|gb|CF025638.1|CF025638
EST:     AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATG                         GTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA
genomic: AAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCA

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), 48 (downstream exon)
Score: 271

TCTTGGCAGACCAATCTTGGGTTCTGCAGAGAATGTCAAGTCAATCACCAAAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 246

TCTTGGCAGACCAATCTTGGGTTCTGCAGAGAATGTCAAGTCAATCACCAAAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 281

TCTTGGCAGACCAATCTTGGGTTCTGCAGAGAATGTCAAGTCAATCACCAAAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 319

TCTTGGCAGACCAATCTTGGGTTCTGCAGAGAATGTCAAGTCAATCACCAAAGAGGACCTTGAGAACTACATTGCAACTCATTATACAGCTCCTAGAATGgtacatgatt ... cacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattttatgttcctgttattggagtatgatggaagtacttttacacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT
                                       cttttac  CT-rich tract
     tttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgatttcaactgtgttgcttctgcaccattttatgttcctgttattggagtatgatggaagtacttttacacgtttcagGTTATCACAGCTGCAGGCAATGTGAAACATGAAGACATTGTTGAGCAGGCAAAGAAGTTGTTCAATAAGCTATCAACTGACCCTACAACAACAAACATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT