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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggaaatgctcagtgatttctcaggatcggaatagttgcttttctcatcattgtttacttcagctaaatctcaacttcttgagttcttgtctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC

Basic information

species Zea mays
transcript GRMZM2G175071_T01
intron # 1
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|76293872|gb|DV033440.1|DV033440
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|149108572|gb|EE292847.2|EE292847
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|149111653|gb|EE190797.2|EE190797
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|74240108|gb|DT648022.1|DT648022
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|148975813|gb|EE025803.2|EE025803
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|71434702|gb|DR815752.1|DR815752
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|50328062|gb|CO523188.1|CO523188
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|149064135|gb|EE286431.2|EE286431
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|60401129|gb|DN233936.1|DN233936
EST:     CCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACCGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: CCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|89763835|gb|DY690863.1|DY690863
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|71430395|gb|DR811445.1|DR811445
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|74237799|gb|DT645713.1|DT645713
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|149010241|gb|EE042063.2|EE042063
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|148969536|gb|EE020363.2|EE020363
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|76013106|gb|DT940276.1|DT940276
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|71772253|gb|DR970190.1|DR970190
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
EST: gi|74235239|gb|DT643153.1|DT643153
EST:     GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAG                         GGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA
genomic: GCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGA

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: 45 (upstream exon), 47 (downstream exon)
Score: 42

GCTCTGGGATGCTCCCAGGCGCCGGGTTCGGCGAGACGGGGAGTCACCACGCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 83

GCTCTGGGATGCTCCCAGGCGCCGGGTTCGGCGAGACGGGGAGTCACCACGCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 77

GCTCTGGGATGCTCCCAGGCGCCGGGTTCGGCGAGACGGGGAGTCACCACGCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC


Block sizes: 34 (upstream exon), 40 (downstream exon)
Score: 23

GCTCTGGGATGCTCCCAGGCGCCGGGTTCGGCGAGACGGGGAGTCACCACGCGGCAGACGCGCCGCCGGCGCTGCCTTGCAGTTCCTCGGGCGATTCAAGgtgagcatcg ... tctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcattgtttacttcagctaaatctcaacttcttgagttcttgtctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC
                 agctaaa  putative branch site (score: 23)
                                       ttcttgtct  putative PPT
     attgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggaaatgctcagtgatttctcaggatcggaatagttgcttttctcatcattgtttacttcagctaaatctcaacttcttgagttcttgtctgtaatagGGAATATTATCAGTGGAAGAGACTGGTGAATCAAAGGCAGTCAACGCTAGATGGAGGCAAAGTGCCTGCTGCATTGGGCCACCATGTTTTTGGTGCGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg