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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattattgaataattgttgtgtcatcgagattgagtacaagttgccaattaaaacctgaaacatggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA

Basic information

species Zea mays
transcript GRMZM2G122937_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122937_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 2
gtaattattgaataattgttg----tgtcatcgagattgagtacaagt-tgccaattaaaacctgaaacatggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA
|| |||||| |||||||   |      || |   |  || ||  || | | ||||| | ||| | |||  ||   | ||||| | |||||||||||||||||||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||||||||||||
gtgattattaaataatttgagacatcttctttttgtctgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
















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|18168286|gb|BM338126.1|BM338126
EST:     GCTCCCGAGAAGCCTGCCCGTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGAAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|211265456|gb|FL003939.1|FL003939
EST:     GCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|16921666|gb|BM075240.1|BM075240
EST:     TGCTCCCGAAAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|211416317|gb|FL076963.1|FL076963
EST:     GCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|13178708|gb|BG349966.1|BG349966
EST:     GCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18172733|gb|BM348121.1|BM348121
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18174754|gb|BM350142.1|BM350142
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18179208|gb|BM380418.1|BM380418
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18180045|gb|BM381255.1|BM381255
EST:     GCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18175084|gb|BM350472.1|BM350472
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|83278839|gb|DV942847.1|DV942847
EST:     CTCCAATGACAGTG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: CTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18172642|gb|BM348030.1|BM348030
EST:     AGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: AGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18165727|gb|BM335566.1|BM335566
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|13381780|gb|BG458335.1|BG458335
EST:     TGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|17930789|gb|BM267749.1|BM267749
EST:     GCTCCCGAGAAGGCCTGCCCATGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGATCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCTCCCGAGAA-GCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|16920671|gb|BM074771.1|BM074771
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18168900|gb|BM338740.1|BM338740
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|28986517|gb|CB351176.1|CB351176
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|17931968|gb|BM268928.1|BM268928
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|148966674|gb|EE017731.2|EE017731
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|15214758|gb|BI431067.1|BI431067
EST:     GGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|28986148|gb|CB350993.1|CB350993
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATAACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|17930420|gb|BM267380.1|BM267380
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18170396|gb|BM340236.1|BM340236
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|149069632|gb|EE158017.2|EE158017
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18167107|gb|BM336946.1|BM336946
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18167362|gb|BM337201.1|BM337201
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18176812|gb|BM351745.1|BM351745
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|148944466|gb|EC889583.2|EC889583
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18174579|gb|BM349967.1|BM349967
EST:     GCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: GCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|60345190|gb|DN212163.1|DN212163
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|18163345|gb|BM333184.1|BM333184
EST:     TGCTCCCAAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCANAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|213171583|gb|FM184654.1|FM184654
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
EST: gi|15100443|gb|BI396234.1|BI396234
EST:     TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGG                         ATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG
genomic: TGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAG

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: 244

AAGTTGCAGATGAACCTGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1949

AAGTTGCAGATGAACCTGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1936

AAGTTGCAGATGAACCTGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 846

AAGTTGCAGATGAACCTGCTCCCGAGAAGCCTGCCCCTGCGAAGCAAGGGGGCTCCAATGACAGGGgtaattattg ... tggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcatcgagattgagtacaagttgccaattaaaacctgaaacatggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA
                            aattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattattgaataattgttgtgtcatcgagattgagtacaagttgccaattaaaacctgaaacatggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA