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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttatctccactattttctcctggtgttgttaaactgggatgactattatcttatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG

Basic information

species Zea mays
transcript GRMZM2G413857_T01
intron # 8
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|32804882|gb|CD957118.1|CD957118
EST:     GATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|71443344|gb|DR824394.1|DR824394
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGGCA-T
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGG-CAAT
EST: gi|26457201|gb|CA828784.1|CA828784
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|71443847|gb|DR824897.1|DR824897
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCT
EST: gi|67023933|gb|CO452682.1|CO452682
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|19351457|gb|BM895989.1|BM895989
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAATGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|67011356|gb|CO440105.1|CO440105
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT

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: 36 (upstream exon), 48 (downstream exon)
Score: 30

GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG


Block sizes: 40 (upstream exon), 38 (downstream exon)
Score: 18

GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 14

GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 180

GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG
                                        tcttcttctgt  CT-rich tract
             aacatgtaaaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatttatctccactattttctcctggtgttgttaaactgggatgactattatcttatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATTAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT