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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatatatttttattgttctcactacatcttaaaaacatttttttattttgtatcatgttacaaataatctaaaattagttattttgtctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA

Basic information

species Zea mays
transcript GRMZM2G126656_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 4
tattatatatttttattgttctcactacatc-ttaaaaacatttttttatt----ttgtatcatgttacaaataatctaaaattagttattttgtctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA
 || |  ||| |    | |||| |||| |   ||| |    ||| |||||     || |||   || |  |  ||| |||  | | |   | | | ||| ||||||||||| |||| |||| ||||||||||| ||||||||||||||||||||| |||||||||| ||||| |||   |||||
-atcaggtatatca--tattct-actagactattatatgtgtttgtttatcataattatatttggtaatgatcaatttaaggt-attctctgtttgtggatacagCTCCTTATGCTTTCATAGAAACTCTAAGAGAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA
















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|71764856|gb|DR962793.1|DR962793
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
EST: gi|71304764|gb|DR788496.1|DR788496
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
EST: gi|211362912|gb|FL253415.1|FL253415
EST:     CAGCTGCTGTTGAAGGGGTCGAAACGTCA-TTAGGAGGGAAACTTT-CAG                         CTCCTTCTGCTCTCATTGAAACT
genomic: CAGCTGCTGTTGAAGGGGTCGAA-CGTCAATTAGGAGGGAA-CTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACT
EST: gi|78086694|gb|DV515087.1|DV515087
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATNGT-CAAACCTTCT
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGAT-GTTCAAACCTTCT
EST: gi|30704520|gb|CD058548.1|CD058548
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
EST: gi|71766059|gb|DR963996.1|DR963996
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
EST: gi|148949419|gb|EC894878.2|EC894878
EST:     AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAG                         CTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC
genomic: AGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTC

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: 47 (upstream exon), 48 (downstream exon)
Score: 15

TATGAAGCAATAGCAAGACTGGAAAAGGCTGCAGAACAAGGAAGTGCAATAGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 29

TATGAAGCAATAGCAAGACTGGAAAAGGCTGCAGAACAAGGAAGTGCAATAGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 16

TATGAAGCAATAGCAAGACTGGAAAAGGCTGCAGAACAAGGAAGTGCAATAGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 11

TATGAAGCAATAGCAAGACTGGAAAAGGCTGCAGAACAAGGAAGTGCAATAGCAGCTGCTGTTGAAGGGGTCGAACGTCAATTAGGAGGGAACTTTTCAGgtttctgcat ... ctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttgtatcatgttacaaataatctaaaattagttattttgtctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA
                        atctaaa  putative branch site (score: 11)
                                       ttttgtct  putative PPT
        tatcatgttacaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatatatttttattgttctcactacatcttaaaaacatttttttattttgtatcatgttacaaataatctaaaattagttattttgtctggttacagCTCCTTCTGCTCTCATTGAAACTCTAAGGGAGAGGATGTTCAAACCTTCTCTGTCAACCATCGTCACAGAGAATACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - ctacatc
- - - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtta