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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacatgtttttcccctaaagcctacctccatgtgtttaaaaacgtctgctttttttcacagccatcgctcttgttcattttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG

Basic information

species Zea mays
transcript GRMZM2G004696_T01
intron # 4
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|28986332|gb|CB351083.1|CB351083
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|166482889|gb|EG100431.1|EG100431
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCGAGAGCCGCCCGA
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGA
EST: gi|18173156|gb|BM348544.1|BM348544
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|113822270|gb|DW938450.1|DW938450
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGG
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGG
EST: gi|18162902|gb|BM332741.1|BM332741
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|31664124|gb|CD573304.1|CD573304
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|29544822|gb|CB605430.1|CB605430
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|31612276|gb|CD568898.1|CD568898
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|18163244|gb|BM333083.1|BM333083
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|31362759|gb|CD447116.1|CD447116
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|18174655|gb|BM350043.1|BM350043
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|211380527|gb|FL436057.1|FL436057
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCGAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCAC--
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|56382192|gb|CV984861.1|CV984861
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|78105144|gb|DV523562.1|DV523562
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|18175256|gb|BM350636.1|BM350636
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|211380526|gb|FL436056.1|FL436056
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCGAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCAC--
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|18163782|gb|BM333621.1|BM333621
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
EST: gi|18168464|gb|BM338304.1|BM338304
EST:     AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGG                         CACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC
genomic: AACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGC

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: 82

GATGTTCGTGGAAACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GATGTTCGTGGAAACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG


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

GATGTTCGTGGAAACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GATGTTCGTGGAAACCTGCCAGCGCCTTCGTCTGATGAAAGGTTCAGAGGCCGTGAACTTGGgtacgtacat ... attttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttaaaaacgtctgctttttttcacagccatcgctcttgttcattttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG
                                    ctcttgttcattttc  CT-rich tract
                  tttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacatgtttttcccctaaagcctacctccatgtgtttaaaaacgtctgctttttttcacagccatcgctcttgttcattttcacagCACCAAGAGCCGCCCGATGAGGCACACTCCGTTGGGCGTTGGCACGCACGCACGCACTGGCGTCTTGAAGGAAAGGGGGAACTCTGCTGGTCTTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA