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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgggtgtgccccttttttctttgtaatataaagatacactgctatcttgcatgttctagagaaaaatgtactacaacttgttgctttttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA

Basic information

species Zea mays
transcript GRMZM5G814159_T01
intron # 6
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|32911170|gb|CF015982.1|CF015982
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACCATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAA-CATGTGGTGAA
EST: gi|78180693|gb|DV551066.1|DV551066
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|148929870|gb|EE285590.2|EE285590
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|6827601|gb|AW331244.1|AW331244
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|71772178|gb|DR970115.1|DR970115
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|110932361|gb|EE152587.1|EE152587
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|18164011|gb|BM333850.1|BM333850
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|32835281|gb|CD974959.1|CD974959
EST:     ACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: ACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|31909455|gb|CD650927.1|CD650927
EST:     TGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: TGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|211513327|gb|FL030343.1|FL030343
EST:     AGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|211122862|gb|FL458470.1|FL458470
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|6851486|gb|AW352496.1|AW352496
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|110190841|gb|EC872739.1|EC872739
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|33091830|gb|CF051824.1|CF051824
EST:     ACTAACATTGACAAGAAG                         ATCGCAGAAGATGAGGTGAAGCAATTCTTTGAGGGAACCATGTGGTGAA
genomic: ACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAA-CATGTGGTGAA
EST: gi|76292409|gb|DV031977.1|DV031977
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|86467992|gb|DY234362.1|DY234362
EST:     AATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|211513328|gb|FL030344.1|FL030344
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|32911777|gb|CF016589.1|CF016589
EST:     ATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACCATGTGGTGAA
genomic: ATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAA-CATGTGGTGAA
EST: gi|32165016|gb|CD670334.1|CD670334
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|14243826|gb|BG841499.2|BG841499
EST:     TGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: TGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|86467993|gb|DY234363.1|DY234363
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAAAAGATGAAGTGAAGCATTTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|32937185|gb|CF042004.1|CF042004
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|32914736|gb|CF019548.1|CF019548
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|37395891|gb|CF635231.1|CF635231
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACTTTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|67021641|gb|CO450390.1|CO450390
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|149099389|gb|EE185429.2|EE185429
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|31362976|gb|CD447333.1|CD447333
EST:     AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
EST: gi|16926655|gb|BM079723.1|BM079723
EST:     AATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAG                         ATCGCAGAAGATAAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
genomic: AATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA

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: 289

ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 244

ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 421

ACTGATGATGAGAAAGAAATGGTATCCAGGACTGTGTATTGTACTAACATTGACAAGAAGgtatgttttg ... ttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttgcatgttctagagaaaaatgtactacaacttgttgctttttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA
                                  cttgttgcttttttt  CT-rich tract
                   aaaaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgggtgtgccccttttttctttgtaatataaagatacactgctatcttgcatgttctagagaaaaatgtactacaacttgttgctttttttgtgtagATCGCAGAAGATGAAGTGAAGCAATTCTTTGAGGGAACATGTGGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - -tacactg
- - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct