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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgagtgcacaaaactataatttctgccttagactctacacaatatcatttgttatatagcatgcttgtaatatgcctaaatcaatgtattgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG

Basic information

species Zea mays
transcript GRMZM2G050460_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050460_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16890.3 (Oryza sativa), 3'ss of exon 2
---gtgagtgcacaaaactataatttctgccttagactctacacaatatcatt-tgttatatagcatgcttgtaatatgcctaaatcaatgtattgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG
   || |       | |  ||     |||| |   || ||||    | |  |  | ||   | |||  ||  ||       |      |||| || |||  |||| ||||||||||||||| |||||||||| || || ||||||||||| |||||||||||||| |||||| |||| ||||| || |||||||| ||||| ||
tgtgtaaacttttcagagcatgg---ctgcatactaccctactttgttttgtcatctttgctggcagactgatatctaatgtccccgcatgtcttcatta-cagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAATTGAGTACTACGCTATGTTGGCCAAGGTCACCGTCCACCATTTCCACGG
















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|211445721|gb|FL164466.1|FL164466
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|15590487|gb|BI675103.1|BI675103
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|18164616|gb|BM334455.1|BM334455
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|211447832|gb|FL164470.1|FL164470
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|60354341|gb|DN221314.1|DN221314
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|44900176|gb|CK826721.1|CK826721
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|60358040|gb|DN225013.1|DN225013
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|18649989|gb|BM498808.1|BM498808
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|4887277|gb|AI677376.1|AI677376
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|15554273|gb|BI644271.1|BI644271
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|71772654|gb|DR970582.1|DR970582
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|45567674|gb|CK985687.1|CK985687
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|32912640|gb|CF017452.1|CF017452
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|45848107|gb|CN072050.1|CN072050
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|17921702|gb|BM259353.1|BM259353
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|9794654|gb|BE552962.1|BE552962
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|19822553|gb|BQ048577.1|BQ048577
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|71439472|gb|DR820522.1|DR820522
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|78027496|gb|DV495883.1|DV495883
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|44681696|gb|CK786744.1|CK786744
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|19057738|gb|BM736405.1|BM736405
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|7227589|gb|AW566230.1|AW566230
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|15590488|gb|BI675104.1|BI675104
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|37378408|gb|CF625893.1|CF625893
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|211445724|gb|FL164469.1|FL164469
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
EST: gi|211445722|gb|FL164467.1|FL164467
EST:     GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGT                         CAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA
genomic: GTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAA

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: 244

TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagc ... tgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttgttatatagcatgcttgtaatatgcctaaatcaatgtattgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG
                                          tattgat  putative branch site (score: 126)
                                                ttttc  CT-rich tract
                                taaatcaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcacaaaactataatttctgccttagactctacacaatatcatttgttatatagcatgcttgtaatatgcctaaatcaatgtattgattttcagCAAAGCTAGTGATCATTGCTAACAACTGTCCTCCGCTTCGGAAGTCTGAAATTGAGTACTATGCTATGCTGGCTAAGGTGACAGTCCACCACTTCCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG