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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatggacatacataaaattttgttggtcctttcatttttgcagaactgacatgattttcactgcctacttctcaaattcgtattgtatctacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169089_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 12
acatggacatacataaaattttgttggtcctttcatttttgcagaactgacatgattttcactgcctacttctcaaattcgtattgtatctacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
| | ||| ||| | | | | | | | | | | | | ||||| ||||||| | ||||||| ||||||||||||| ||||| ||||||||||| ||||||||||||| ||| ||||||
gatttgttatattgctcattgtacagaacaaatgtgatctctctcttttttttaaaaaaaaatacatactttccaaattcatggtgtatcttcactgcagGGTGTTGCTATCCTAATCTCGTTCCTGGTTTCAGCTGCATTTCATGAG
















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|18164197|gb|BM334036.1|BM334036
EST:     CATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: CATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|17930011|gb|BM266971.1|BM266971
EST:     TTTTCCATGTATAAGAAAAGGCTTTTCCAGGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: TTTTCCATGTATAAGGAAAGGCTTTTCCA-GGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|18165097|gb|BM334936.1|BM334936
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCA-GGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|32929949|gb|CF034761.1|CF034761
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGGTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|18172967|gb|BM348355.1|BM348355
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|113703224|gb|EE680728.1|EE680728
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|261490382|gb|GO359873.1|GO359873
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|18168645|gb|BM338485.1|BM338485
EST:     ATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: ATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|18171503|gb|BM341343.1|BM341343
EST:     GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: GGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|16921463|gb|BM075161.1|BM075161
EST:     ATCATCAGACACATATATCTTCCATGTATAAGGAAAGGCTTTTCCAGG                         GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: ATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|17930787|gb|BM267747.1|BM267747
EST:     ATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTTCAGG                         GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: ATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
EST: gi|18166675|gb|BM336514.1|BM336514
EST:     AAGGCTTTTCCAGG                         GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
genomic: AAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG

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: 43 (upstream exon), 47 (downstream exon)
Score: 18

CCTGTTCATAAGTGGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 31

CCTGTTCATAAGTGGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 39

CCTGTTCATAAGTGGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 22

CCTGTTCATAAGTGGATCATCAGACACATATATTTTCCATGTATAAGGAAAGGCTTTTCCAGGgtaattgctt ... tacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgacatgattttcactgcctacttctcaaattcgtattgtatctacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG
 aactgac  putative branch site (score: 22)
 atgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatggacatacataaaattttgttggtcctttcatttttgcagaactgacatgattttcactgcctacttctcaaattcgtattgtatctacactgcagGGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
-catggac
- - - - - acataaa
- - - - - - - - - - -tgttggt
- - - - - - - - - - - - - - -ctttcat
- - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcactg