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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggacggatattcttatattccttcaaacatgagattgaaacactaacacatttctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG

Basic information

species Zea mays
transcript GRMZM2G146472_T03
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|89248294|gb|DY620080.1|DY620080
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062369|gb|FL252799.1|FL252799
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062365|gb|FL252795.1|FL252795
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211179476|gb|FL252803.1|FL252803
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211059403|gb|FL252784.1|FL252784
EST:     TCCGCTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062364|gb|FL252794.1|FL252794
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062361|gb|FL252791.1|FL252791
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|149078577|gb|EE167361.2|EE167361
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062368|gb|FL252798.1|FL252798
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: -CTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|149109057|gb|EE189984.2|EE189984
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062371|gb|FL252801.1|FL252801
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTG
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTG
EST: gi|211062360|gb|FL252790.1|FL252790
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062359|gb|FL252789.1|FL252789
EST:     TCTGTTGATATCACAGACACATGGGAAC-TTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCAMTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062367|gb|FL252797.1|FL252797
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062362|gb|FL252792.1|FL252792
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211059404|gb|FL252785.1|FL252785
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|29945425|gb|CB815632.1|CB815632
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211062366|gb|FL252796.1|FL252796
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
EST: gi|211059402|gb|FL252783.1|FL252783
EST:     TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC                         ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA
genomic: TCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAA

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: 1055

AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1280

AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 983

AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 605

AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggacgg ... ctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttatattccttcaaacatgagattgaaacactaacacatttctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG
                                cactaac  putative branch site (score: 605)
                                        catttct  CT-rich tract
     tatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggacggatattcttatattccttcaaacatgagattgaaacactaacacatttctgtacacagACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC