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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgttgaatggacatcagaaatgtacattcgccagctgatgcatcttacatggtgtattcatgcttcgtatatttccctgaccattttttgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG

Basic information

species Zea mays
transcript GRMZM2G041633_T01
intron # 10
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|32866957|gb|CF006639.1|CF006639
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|7227682|gb|AW566323.1|AW566323
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|32866956|gb|CF006638.1|CF006638
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|211322922|gb|FL468804.1|FL468804
EST:     TGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGSCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: TGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|6563866|gb|AW231488.1|AW231488
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|7216790|gb|AW562912.1|AW562912
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|13515616|gb|BG517892.1|BG517892
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|67023650|gb|CO452399.1|CO452399
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|37381633|gb|CF627713.1|CF627713
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|13558398|gb|BG549754.1|BG549754
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
EST: gi|6742334|gb|AW313149.1|AW313149
EST:     ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATG                         AAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA
genomic: ATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCA

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), 49 (downstream exon)
Score: 147

GATCAGGAGCAGTCATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

GATCAGGAGCAGTCATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GATCAGGAGCAGTCATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 99

GATCAGGAGCAGTCATTACTTGATGCAATTGCCAGACTTGATGAAGCATCTGATAGCGATAATGgtaagttcct ... tgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacatggtgtattcatgcttcgtatatttccctgaccattttttgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG
                               ccctgac  putative branch site (score: 99)
                                     ccatttttt  CT-rich tract
                                       attttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgttgaatggacatcagaaatgtacattcgccagctgatgcatcttacatggtgtattcatgcttcgtatatttccctgaccattttttgtgttacagAAGATATGGCCATGGAAGGCCGAATGGGTTCTGCTGGGGAAAGGAATGGCATCACTACGTAGTTGCTTCTGGCATGTTGGAATTTTGGTAGATTAACATG

- - ttgaatg
- - - - - - - - - - - - - - - - - -gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgc