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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaaaaaatctttagtccaaatatttgataccttttttatccaataatgtgaaatgtcctaaaacttcactttccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC

Basic information

species Zea mays
transcript GRMZM2G463913_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
gtgagtaaaaaaaatctttagtccaaatatttgataccttttttatccaataatgtgaaatgtcctaaaacttcactttccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
|| |||   ||   | ||| |  |      ||| ||     ||||  |||   | |||||| |||        |  |||||| ||||||||||| |||||||| | ||||||||||||||||||||||||||||| ||||||||||||||||||||||| || || || ||||| || ||||||||||
gtaagtttcaattcttttttggtctgcagcttgcta-----tttactcaaatgtctgaaatttcc--------ctttttccaatgcagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC

upper sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
--gtgagtaaaaaaaatctttagtccaa---atatttga-taccttttttatccaa---taatgtgaaatgtcctaaaacttcactttccact---gcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
   |     |||| | | | ||| |  |   ||| |  | ||  || | || | |    ||||||    |||  || |  |||  ||||  ||   |||||||||  |||||||||| ||| ||||||||||||||||||||||| |  ||||||| ||||||||||   | || || ||||| || || ||  | || |
ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC

upper sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G36150.1 (Glycine max), 3'ss of exon 2
-----gtgagtaaaaaaaatctttagtc-caaatatttgataccttttttatccaataatgtgaaatgtcct----aaaacttcactt-tccactg-cagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
      |    ||| |  || | ||| |  |  |||     |  | | ||||  |   |     |||||  |    || | ||   || ||| ||| ||||||||  ||||||| || ||| |||||||||||||||| |||||| |  ||||||| ||||||||||   | || || ||||| || || ||  | || |
tttatattgcaaaacagcatatctaggcatagttatactcaaaatatattatgtagctagccttaatgttttgtgtaatattttgtttctcctctggcagCTTAAACGATGGGAACGGAAGGAGTGTAAACCAAACAGCCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC

upper sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0014g04970.t01 (Vitis vinifera), 3'ss of exon 2
----gtgagtaa---aaaaaatctttagt--ccaaatatttgatacctt--ttttatccaataatgtgaaatgtcctaaaacttcactttccac-tgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
     |||| ||   |||||  | | |||  |   ||  |    | | |   ||     || |||   || ||   | |   |    || || | ||||||||||| |||||||||| ||| | || ||||| ||||| ||||| ||||| || || |||||||||| | | || || || ||  |  | ||  | ||  
ctgtctgagcaacgcaaaaatccatgagttacttgatgatcatgaacatggcttctcttaaaaataccaagtggttttactttgtctttacctcatgcagCTTAAGCGATGGGAGCGGAAGGAATGCAAACCCAACAGCCTTCCGGTGCTACATAAAATGCATGTTAAGGTGGGAGATACAGTGAAAATAATATCTGGTA

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|211412838|gb|FL137855.1|FL137855
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGCMAGTGTAAACCAAACAGTCTTCCTGTGCT
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGA-AGTGTAAACCAAACAGTCTTCCTGTGCT
EST: gi|211002601|gb|FL137895.1|FL137895
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415391|gb|FL137870.1|FL137870
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415389|gb|FL137868.1|FL137868
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417930|gb|FL137880.1|FL137880
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415392|gb|FL137871.1|FL137871
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417933|gb|FL137883.1|FL137883
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417927|gb|FL137877.1|FL137877
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417935|gb|FL137885.1|FL137885
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417928|gb|FL137878.1|FL137878
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415393|gb|FL137872.1|FL137872
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417934|gb|FL137884.1|FL137884
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415387|gb|FL137866.1|FL137866
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211002597|gb|FL137891.1|FL137891
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417931|gb|FL137881.1|FL137881
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211144491|gb|FL281167.1|FL281167
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211412840|gb|FL137857.1|FL137857
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211415390|gb|FL137869.1|FL137869
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211417932|gb|FL137882.1|FL137882
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211002596|gb|FL137890.1|FL137890
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|15199031|gb|BI423618.1|BI423618
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|211002603|gb|FL137897.1|FL137897
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
EST: gi|161407369|gb|DW042372.1|DW042372
EST:     GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGA                         CTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG
genomic: GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 202

GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 2225

GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 40

GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 381

GTAAGGTTTATGGTCAAGATATGCCCAATTGAAATGAGAgtgagtaaaa ... tccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccttttttatccaataatgtgaaatgtcctaaaacttcactttccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
                             tcctaaa  putative branch site (score: 381)
                                     cttcactttccact  CT-rich tract
     ttttttatccaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaaaaaaatctttagtccaaatatttgataccttttttatccaataatgtgaaatgtcctaaaacttcactttccactgcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG