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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttattacttctctggttgagaacagttgatctcttataagttctataagcttatgcatttgtactgctaagttaaatttggatgtcttctcgatg...

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 10
GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagtta-ttacttctctggttgagaacagttgatctcttataagttctataagcttatg-catttgtactgctaagttaaatttg-gatgtcttctcgatg
|| ||||| || ||||| || || |||||||||||||| || |||||||||||||||||||||||||||||||||  || | || || || | |||     |       |    | || |   ||||  |||    |  |  |    ||| | ||||    ||||   |||     
GTTCCACTGTCGAGTGTAAAGGGAACTGGTCCTGATGGGCGCATTTTGAAGGCAGACATTGAAGATTACTTGGgtatgtcactttctcctatagttcccccccccccccccaaaaaaaataaaataaaattaaaataaataaataaataaataaaataaatgatgaactctat---

upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 10
GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttattacttctctggttgagaacagttgatctcttataagttctataagcttatgcatttgtactgctaagttaaatttggatgtctt-ctcgatg
|| ||||| ||||| || |  || |||||||||||||| || ||||||||||| |||||||||||||||||||||  |   || ||  | |       | |      |||||      ||||     ||||   ||     ||||   |  ||||     |  ||   |  || 
GTTCCACTGTCAAGCGTAATGGGAACTGGTCCTGATGGGCGAATTTTGAAGGCGGACATTGAAGATTACTTGGgtatgccctttctcttgtcccctccacccccct-tctctctctctttctcctcccttaatgatgaaatctgcgtggaaaaatgcaattaactagttttata

upper sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 10
GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttattacttctctggttgagaacagttgatctcttataagttctataagcttatgcatttgtactgctaagttaaatttggatgtcttctcgatg--
|| || ||   |||  | ||||| || ||||||||||| || ||| ||||||| || ||||||||||| ||||||  | | ||   | | || ||  | |   ||   || |||   | |  || |  |||   |  |  |     || |         |||   |||  |    
GTTCCTCTTCAAAGCATCAAAGGGACGGGTCCTGATGGACGCATTGTGAAGGCTGATATTGAAGATTATTTGGgtatgcttttctctatgtgcttttgca-gattatcctgttacttgcttgattaatttagctagata-atcaacaattatggagacaatgctgtcttaagtac

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|74235054|gb|DT642968.1|DT642968
EST:     TACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGG                         CTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAG
genomic: TACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAG
EST: gi|32840355|gb|CD980036.1|CD980036
EST:     CCTGATGGCCGTATTTTGAAGGCAGACATTGAAGATTACTTGG                         CTTCTGTAGCCAAGGGTGGGTTGAGGGAGGCTTTTGCAGATCCAGGGTTAG
genomic: CCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAG
EST: gi|32938642|gb|CF043461.1|CF043461
EST:     TACTGGTCCTGATGGCCGTATTTTGAAGGCAGACATTGAAGATTACTTGG                         CTTCTGTAGCCAAGGGTGGGTTGAGGGAGGCTTTTGCAGATCCAGGGTTAG
genomic: TACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAG
EST: gi|32932311|gb|CF037123.1|CF037123
EST:     ACTGGTCCTGATGGCCGTATTTTGAAGGCAGACATTGAAGATTACTTGG                         CTTCTGTAGCCAAGGGTGGGTTGAGGGAGGCTTTTGCAGATCCAGGGTTAG
genomic: ACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 134

GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 285

GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 213

GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 296

GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttatt ... cttaatgaagCTTCTGTAGCCAAGGGTGGGCTGAGGGAGTCTTTTGCAGATCCAGGGTTAGGTTATGTTGATATTCCAAATGCACAGATAAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCACTATCAAGTGTGAAAGGTACTGGTCCTGATGGTCGTATTTTGAAGGCAGACATTGAAGATTACTTGGgtgagttattacttctctggttgagaacagttgatctcttataagttctataagcttatgcatttgtactgctaagttaaatttggatgtcttctcgatg

- - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA