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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaagaggacaatcaaccatcaagtctaagatgcctagcctaacaactactgttccttcactgtgttgattttattgctaattttggtaaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 10
---ttctaagaggacaatcaaccatcaagtctaagatgcctagcctaacaactactgttccttcactgtgttgattttattgctaattttggtaaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
      |     | |  | ||     | |   |   |        | | | | | |||  ||||| ||   |    | |||  | |   |   ||   | ||||| ||||| ||||||||| |||||||||| || ||||||||||| || || ||||||||||||||||| ||||| || ||||||||||||||||| || |
ctgccattctctgcccttgaatttatatgatcagtgttttcgaattcata-ccagtgtaacttca-tgcaatatgctgattaatcaccattacaatt-tacagCTCGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAG
















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|19770441|gb|BQ035162.1|BQ035162
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|71760908|gb|DR958845.1|DR958845
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|211091500|gb|FL454775.1|FL454775
EST:     TAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: TAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|5917508|gb|AW054311.1|AW054311
EST:     AGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCNCATGCG
genomic: AGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|89251547|gb|DY623333.1|DY623333
EST:     TATTCACCAAATTTAAGATGCACTGTT                         CTTGAAGCGTGGGCACATCCATTCTTTGGCGATTTGCGAGAACCACATGCG
genomic: TATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     TCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGNCT                         CTTGAAGCGTGTGCACATCCATTTCTTTGACGATTTG
genomic: TCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTG-CTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATT-CTTTGACGATTTG
EST: gi|4887444|gb|AI677543.1|AI677543
EST:     TCGCTTCACGCTTGCTCCAGTATTCGCCAAATTTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: TCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|32808410|gb|CD960644.1|CD960644
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     TCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGNCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGC
genomic: TCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTG-CTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGC
EST: gi|71430637|gb|DR811687.1|DR811687
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|149107144|gb|EE189033.2|EE189033
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGGGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|30031860|gb|CB833711.1|CB833711
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|71596046|gb|DR906797.1|DR906797
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|110961978|gb|EE182030.1|EE182030
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|76922776|gb|DV169168.1|DV169168
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|60338092|gb|DN205065.1|DN205065
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|110194431|gb|EC876329.1|EC876329
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|211304345|gb|FL459464.1|FL459464
EST:     TGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: TGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|87153591|gb|DY398380.1|DY398380
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|20300620|gb|BQ163563.1|BQ163563
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|76287881|gb|DV027449.1|DV027449
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|60350723|gb|DN217696.1|DN217696
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|60358944|gb|DN225917.1|DN225917
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|148952786|gb|EC898772.2|EC898772
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATTTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|31352553|gb|CD436910.1|CD436910
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|12970789|gb|BG267159.1|BG267159
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG
genomic: ATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCG

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: 48 (upstream exon), 48 (downstream exon)
Score: 371

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 425

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 352

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 231

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCTgtgagttttg ... aaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactactgttccttcactgtgttgattttattgctaattttggtaaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
                                         tggtaac  putative branch site (score: 231)
                         attttattgctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaagaggacaatcaaccatcaagtctaagatgcctagcctaacaactactgttccttcactgtgttgattttattgctaattttggtaaccatgcagCTTGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG

- - - - - - - tcaacca
- - - - - - - - - - - - - - - - -tgcctag
- - - - - - - - - - - - - - - - - - - - - -aacaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttggt