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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtttagcatcaggaacctttgtgtttatttctatacatatttgcgaagcacagtgacaatactataattttgataactgttttgtgatttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 3
tatgtttagcatcaggaacctt---tgtgtttatttctatacatatttgcgaagcacagtgacaatactataattttg----------ataactgttttgtgatttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG
            || | | |||   | ||||| ||| | | ||  |||   ||| | | || || |||||||||  ||           ||| |  | || | |||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| ||||||||||| || ||||||||||
------------caaggatcttgcctttgtttctttgtttgca-gtttattaagtaaaatggcattactataatcatgttctttttccctaagtcctatgcggtttggtgcagGAATTCTTTGATGCAGAAATAAAAAAGCTGAAGCTGAAACCTTATTATTTCCCATTGTTTGTCACTGAGAATGTCCTACAGAAGGAGAAAGACCACATTG
















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|71332073|gb|DR802941.1|DR802941
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|15312974|gb|BI478491.1|BI478491
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|6865183|gb|AW360533.1|AW360533
EST:     AATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: AATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|211280528|gb|FL042846.1|FL042846
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|67027739|gb|CO456488.1|CO456488
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|211280526|gb|FL042844.1|FL042844
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|211280529|gb|FL042847.1|FL042847
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|32929788|gb|CF034600.1|CF034600
EST:     GTTGTTATATATTGAGGCCATGGGCAATGGAAATCTGGGAGCTAATGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|148961334|gb|EE012063.2|EE012063
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCANACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
EST: gi|211280527|gb|FL042845.1|FL042845
EST:     GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA                         GAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC
genomic: GTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTC

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: 733

GTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 710

GTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 544

GTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 549

GTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAAgtaagtttat ... tttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgaagcacagtgacaatactataattttgataactgttttgtgatttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG
                            tgataac  putative branch site (score: 549)
             acaatactataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtttagcatcaggaacctttgtgtttatttctatacatatttgcgaagcacagtgacaatactataattttgataactgttttgtgatttggtgcagGAATTCTTTGATGCAGAAATTAAAAAGCTGAAGCTCAAACCATATTATTTCCCTTTGTTTGTTACTGAGAATGTTCTACAGAAGGAAAAGGACCACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - gcatcag
- - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - -gaagcac