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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactagcccttaatgattatttgatcaaaaactcaacactagctgcttcagatgagaaatgtcactggtgataacacctctttttcatcatcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG

Basic information

species Zea mays
transcript GRMZM2G150251_T02
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|91870069|gb|EB400685.1|EB400685
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|32797772|gb|CD950008.1|CD950008
EST:     GATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: GATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|32803071|gb|CD955307.1|CD955307
EST:     GATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: GATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|60349110|gb|DN216083.1|DN216083
EST:     CGGGGTCAACAGCAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|32796372|gb|CD948608.1|CD948608
EST:     GATCCGGTGACTGACCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: GATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|76020573|gb|DT947743.1|DT947743
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211139849|gb|FK978970.1|FK978970
EST:     GGGGTCGACAACAGCTCGAGATCCGGTGACTGATACTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: GGGGTCGACAACAGCTCGAGATCCGGTGACTGAT-CTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|76282341|gb|DV021909.1|DV021909
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211139848|gb|FK978969.1|FK978969
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138916|gb|FK978964.1|FK978964
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138918|gb|FK978966.1|FK978966
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138912|gb|FK978960.1|FK978960
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211139847|gb|FK978968.1|FK978968
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|30031840|gb|CB833691.1|CB833691
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138913|gb|FK978961.1|FK978961
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138914|gb|FK978962.1|FK978962
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138919|gb|FK978967.1|FK978967
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|32800677|gb|CD952913.1|CD952913
EST:     GATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: GATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|211138917|gb|FK978965.1|FK978965
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
EST: gi|93282675|gb|EB674939.1|EB674939
EST:     CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCG                         GGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG
genomic: CGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATG

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), 48 (downstream exon)
Score: 91

CTTCGCCGCCCGCGCCAATACTTTCCTCTGCCGGGGCTGCACCGGCAGCGCGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

CTTCGCCGCCCGCGCCAATACTTTCCTCTGCCGGGGCTGCACCGGCAGCGCGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

CTTCGCCGCCCGCGCCAATACTTTCCTCTGCCGGGGCTGCACCGGCAGCGCGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

CTTCGCCGCCCGCGCCAATACTTTCCTCTGCCGGGGCTGCACCGGCAGCGCGGGGTCGACAACAGCTCGAGATCCGGTGACTGATCTCCTTTGTTTCTCGgtgagtaatc ... atcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcagatgagaaatgtcactggtgataacacctctttttcatcatcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG
                        tgataac  putative branch site (score: 85)
                                cctctttttcatcatc  CT-rich tract
                                    tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactagcccttaatgattatttgatcaaaaactcaacactagctgcttcagatgagaaatgtcactggtgataacacctctttttcatcatcttggcagGGCATCTTGCTAGTCTTCTTCCAGATTGCTTCCTAATAATGATGACACATGAATGGGCTGCCAATTTGGCTCTTGCTG

- - - - - - - - - - - -gatcaaa
- - - - - - - - - - - - - - - aactcaa
- - - - - - - - - - - - - - - - - - - - - gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtga