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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaatataacaagtgtatatttgttgttgcataaaaaacaaagttagattctgagaattttattcattgacatgtttgtttttgtatataccttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 4
--------tgcaatataacaagtgtatatttgttgttgcataaaaaacaaagttagattctgagaattttattcattgacatgtttgtttttgtatataccttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
         | | |  | ||  ||    |    |  |||||||   | |   ||||  |   |    |||  | ||| ||||||||   || || |||   ||| ||| |||||||||| |||||||||||||||||| ||||||
caaatcagcgtattccatcacatgctcctgcaatcctgcataatctatac--ttagcgttcca----tttgattattaacatgttttccttggtgtatg--tttgcagACAATGGTGAAGTCATTTGAAGTTTCAGAATTGCCAG
















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|18655015|gb|BM499820.1|BM499820
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|78122343|gb|DV540727.1|DV540727
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAAAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18654986|gb|BM499791.1|BM499791
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|22489991|gb|BU049914.1|BU049914
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18655044|gb|BM499849.1|BM499849
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18655016|gb|BM499821.1|BM499821
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18662028|gb|BM501705.1|BM501705
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|32930849|gb|CF035661.1|CF035661
EST:     ACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: ACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|89106409|gb|DY576626.1|DY576626
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18655043|gb|BM499848.1|BM499848
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGT-GAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18654807|gb|BM499612.1|BM499612
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|22489999|gb|BU049922.1|BU049922
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18649626|gb|BM498445.1|BM498445
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|32933566|gb|CF038378.1|CF038378
EST:     ACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCGTTTGAAGTTTCAGAACTGCCAG
genomic: ACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
EST: gi|18661996|gb|BM501688.1|BM501688
EST:     TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAG                         GCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
genomic: TGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG

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: 128

GATCCTGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GATCCTGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

GATCCTGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GATCCTGTCGAGTCTGTACTCGGGGAGTGTCTGCATCTGGGATTATCAAGCACAGgtaaggccgt ... accttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattctgagaattttattcattgacatgtttgtttttgtatataccttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG
                    cattgac  putative branch site (score: 138)
                                            taccttttc  putative PPT
                              tttgtttttgtatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaatataacaagtgtatatttgttgttgcataaaaaacaaagttagattctgagaattttattcattgacatgtttgtttttgtatataccttttcagGCAATGGTGAAATCATTTGAAGTTTCAGAACTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatg