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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagctgtagtatactagatgtttcattagatatacgttgattctttattcttgatataatcttgtccagccatctgatgtagatcttcttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC

Basic information

species Zea mays
transcript GRMZM2G068259_T01
intron # 13
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|211432678|gb|FK992875.1|FK992875
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432676|gb|FK992873.1|FK992873
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432672|gb|FK992869.1|FK992869
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432669|gb|FK992866.1|FK992866
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211055443|gb|FK991550.1|FK991550
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432674|gb|FK992871.1|FK992871
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432679|gb|FK992876.1|FK992876
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211055441|gb|FK991548.1|FK991548
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432670|gb|FK992867.1|FK992867
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211055439|gb|FK991546.1|FK991546
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211432675|gb|FK992872.1|FK992872
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211055440|gb|FK991547.1|FK991547
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
EST: gi|211055442|gb|FK991549.1|FK991549
EST:     AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAG                         GTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA
genomic: AACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 28

TTTGTTGCTCTTATGCCACTCTTTGATCCTCCAAGGCATGACAGTGCAGAAACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC


Block sizes: 35 (upstream exon), 20 (downstream exon)
Score: 2

TTTGTTGCTCTTATGCCACTCTTTGATCCTCCAAGGCATGACAGTGCAGAAACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC


Block sizes: 44 (upstream exon), 31 (downstream exon)
Score: 9

TTTGTTGCTCTTATGCCACTCTTTGATCCTCCAAGGCATGACAGTGCAGAAACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 58

TTTGTTGCTCTTATGCCACTCTTTGATCCTCCAAGGCATGACAGTGCAGAAACAATACGAAGGGCATTGAACCTTGGTGTTAGTGTAAAAATGATCACAGgtacaccccc ... ttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattcttgatataatcttgtccagccatctgatgtagatcttcttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC
                            atctgat  putative branch site (score: 58)
                                        tcttcttttttcc  putative PPT
       ttgatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagctgtagtatactagatgtttcattagatatacgttgattctttattcttgatataatcttgtccagccatctgatgtagatcttcttttttccagGTGATCAGCTAGCAATTGGGAAGGAAACAGGACGTCGCTTAGGCATGGGTACTAACATGTACCCTTCCTCTGCTTTGCTGGGACAGAATAAGGATGAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - gctgtag
- - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt