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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctcattcacaattttatatgtttgtttgttcgttgttacagctgaactgcacatgcagtttgaaacatgctgttactgatgtgtttgtctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC

Basic information

species Zea mays
transcript GRMZM2G096972_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096972_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g04480.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------ctgctcattcacaattttatatgtttgtttgttcgttgttacagctgaactgcacatgcagtttgaaacatgctgttactgatgtgttt--gtctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC
                                                                               ||  || || | ||| |  | | |  | | |     || ||       |||    | |||| |    || || |   | |  ||||  || |||| ||||||||||| |||||||| ||||| ||||||| ||| |||||||||||||||||||| ||||||||||| ||||| || ||||||||||| ||||||||||
gtgatatattattttttttgtttagattagctagtatgtcaaccaacacagatattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGATATGCAAAGGAAGATTGCCGATGAACTCGACAGAACTCCTGGTGAAATCC
















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|148953887|gb|EC899266.2|EC899266
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATTTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|5055564|gb|AI734451.1|AI734451
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|67024917|gb|CO453666.1|CO453666
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|211543317|gb|FL433017.1|FL433017
EST:     GAAGAGATCACATGGCTTACAGATCTGCCTATTTYCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: GAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|113703143|gb|EE680647.1|EE680647
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|32792660|gb|CD944896.1|CD944896
EST:     GATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: GATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|32930220|gb|CF035032.1|CF035032
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTC
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTC
EST: gi|148972894|gb|EE023905.2|EE023905
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|91872410|gb|EB402367.1|EB402367
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|211407732|gb|FL367080.1|FL367080
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|91872411|gb|EB402368.1|EB402368
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|67017300|gb|CO446049.1|CO446049
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|33091457|gb|CF051451.1|CF051451
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|32808561|gb|CD960795.1|CD960795
EST:     GATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: GATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|211164200|gb|FL365726.1|FL365726
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|86470448|gb|DY236818.1|DY236818
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGAT
EST: gi|32931216|gb|CF036028.1|CF036028
EST:     TGTGTGGAAGAGATCACATGGCTTACAGATCTGTCTATTTTCCAGTGAAG                         GATGTGATAGATGGTGATCTCTGCGAGCAGGTATCCCTCCCTCCCAGCTGA
genomic: TGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAG-TATCCCTCCCTCCCAGCTGA

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: 199

TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 79

TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatgtt ... tctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactgcacatgcagtttgaaacatgctgttactgatgtgtttgtctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC
                               tactgat  putative branch site (score: 83)
                                         tttgtct  putative PPT
                tttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctcattcacaattttatatgtttgtttgttcgttgttacagctgaactgcacatgcagtttgaaacatgctgttactgatgtgtttgtctgttacagGATGTGATAGATGGTGATCTCTGCGAGCAGTATCCCTCCCTCCCAGCTGATATGCAGAGGAAGATTGCTGATGAGCTGGACAGAACTCCGGGTGAAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - -cattcac
- - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - acagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt