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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaggacaatgttgtaatgcatcaaccatcaagtctgagatgcctagcctaaccaactcctgctgtgattttattgctaattttggtagctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG

Basic information

species Zea mays
transcript GRMZM2G151916_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 10
taagaggacaatgttgtaatgcatcaaccatcaa-gtctgagatgcctagcctaaccaactcc-tgctgtgattttattgctaattttggtagctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
        |  ||   |      |  |  ||||  || |  ||   |   ||     |||| | |||  |    | |||  | |   |   |  |  | ||||| ||||| ||||||||| ||||||||||||| |||||||| || || || ||||||||||||||||| ||||| || ||||||||||||||||| || |
ctgccattctctgcccttgaatttatatgatcagtgttttcgaattcataccagtgtaacttcatgcaatatgctgattaatcaccattacaatt--tacagCTCGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAG

upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 10
taagaggacaatgttgtaatgcatcaaccatcaagtctgagatgcctagcctaaccaactcctgctgtga-ttttattgctaattttggtagctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
                                     | || | |    || || |  |  ||     |     |    ||  |  |  ||    |  ||||| ||||||  |||||| |||||||||||||||||||| || ||  |  |  |  | |||||||| || ||  | || || |||| ||| || || ||  
------------------------------------gtaagtttctc--ccaaatcgtccactttgaagggccctgacactggtggta-tacacttcacagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 10
taagaggacaatgttgtaatgcatcaaccatcaagtctgagatgcctagcctaaccaactcctgctgtgattttattgctaattttggta-gctctt-gcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
                                         | |  |  || ||      |    ||  |    | ||  | |  |||||  | |||  ||||| ||||||  |||||| |||||||||||||||||||| || ||  |  |  |  | |||||||| || ||  | || || |||| ||| || || ||  
---------------------------------------gtaagtttctcccaaatcgtccactttg-aagagcactgacactggtggtatacacttcacagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

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|60348444|gb|DN215417.1|DN215417
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|32908149|gb|CF012962.1|CF012962
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|31363416|gb|CD447773.1|CD447773
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|60398739|gb|DN231555.1|DN231555
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|211033507|gb|FL333369.1|FL333369
EST:     TCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGGCT                         CTTGAAGCGTGTGCACATCCATTCCTTTGATGAGTTGC
genomic: TCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTG-CTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTC-TTTGATGAGTTGC
EST: gi|91875587|gb|EB405544.1|EB405544
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|60349644|gb|DN216617.1|DN216617
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|60400988|gb|DN233795.1|DN233795
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|18172689|gb|BM348077.1|BM348077
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|32791784|gb|CD944020.1|CD944020
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|78545004|gb|DV622502.1|DV622502
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|20802617|gb|BQ293667.1|BQ293667
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATATAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|32808982|gb|CD961216.1|CD961216
EST:     ATCTCGCTTCACGTTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|211420812|gb|FL269789.1|FL269789
EST:     ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: ATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|211159258|gb|FL355922.1|FL355922
EST:     TCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGNCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGC
genomic: TCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTG-CTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGC
EST: gi|29545134|gb|CB605312.1|CB605312
EST:     CTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: CTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
EST: gi|95107793|gb|EB740022.1|EB740022
EST:     CGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCT                         CTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG
genomic: CGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCG

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: 142

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 155

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 212

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGTTTGCTCCAGTACTCACCAAATCTAAGATGCACTGCTgtgagtattt ... gctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcctaaccaactcctgctgtgattttattgctaattttggtagctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG
                               tgctaat  putative branch site (score: 119)
                                              ctcttgc  putative PPT
                        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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagaggacaatgttgtaatgcatcaaccatcaagtctgagatgcctagcctaaccaactcctgctgtgattttattgctaattttggtagctcttgcagCTTGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGG

- - - - - -tgttgta
- - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - tgcctag
- - - - - - - - - - - - - - - - - - - - - - - - - ctaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttggt