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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagattgggaatattgtttaaccatcttaacttagtctcttctggcaggactctttctgctgaaaggatatcagtaagctagacatgctaactaggtgttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
gtaaagattgggaatattgtttaaccatcttaacttagtctcttctggcaggactcttt-ctgctgaaaggatatcagtaag---ctagaca-tgctaactaggtgttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC
                    | |||  |  ||       ||   ||| || |||| ||| |||  ||   | |   | ||||   |||     || |    |  | |  ||| |||| |||||||||||||| ||||||||||| |||  |||||| || |||||| ||||||||||||| || |||||||  ||| | |||||||||||||| |
-------------------gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 10
gtaaagattgggaatattgtttaaccatcttaacttagtctcttctggcaggactctttctgctgaaaggatatcagtaagctagacatgctaactaggtg--ttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC
                                        |  | |   |  | | || |            |||  |  ||| |  || || |  |   |  ||||| ||||| || ||||| ||||||||||||||| | |||  |||||||||||||||  |   |  ||||||   ||| ||   |||| ||| |   ||||  ||||
--------------------------------------gtttgtatattaaaatttttacc-----------atcgtttcgcttgtgattcttagcaaaagatttattccagGTTGCCAAAATCGAAACCGAGAAAATGTTGATTTCCATGGTGGAAACTGAGTTATTGCGGAGAAAACAAGAAGGATCATACACTGGAAGCTTCAAGGGGC
















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|67015202|gb|CO443951.1|CO443951
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32826654|gb|CD966332.1|CD966332
EST:     GATCTCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: GATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|67014773|gb|CO443522.1|CO443522
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|67014279|gb|CO443028.1|CO443028
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|31348678|gb|CD433035.1|CD433035
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAAATTGAAACCGAGAAAATGCTCATTACCATGGTGGAAACTGA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAA-TTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGA
EST: gi|32801608|gb|CD953844.1|CD953844
EST:     GATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: GATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|211507301|gb|FK969868.1|FK969868
EST:     CTATTCAGGAGCAACTTATGCTTGANAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAARTTGARACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|6021533|gb|AW066461.1|AW066461
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32831581|gb|CD971259.1|CD971259
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32804076|gb|CD956312.1|CD956312
EST:     GATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: GATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32795214|gb|CD947450.1|CD947450
EST:     CCCATGGCAATGTTCAG                         GTTGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|31353849|gb|CD438206.1|CD438206
EST:     CTATTCATGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32804299|gb|CD956535.1|CD956535
EST:     GATCCTCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: GATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32801889|gb|CD954125.1|CD954125
EST:     GATCCTCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: GATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
EST: gi|32908579|gb|CF013392.1|CF013392
EST:     CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAG                         GTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA
genomic: CTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAA

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: 630

AAGCAAGCTTCAGCCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAATACTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 804

AAGCAAGCTTCAGCCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAATACTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 683

AAGCAAGCTTCAGCCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAATACTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 849

AAGCAAGCTTCAGCCTGAATCAAGGGAGCTGTTTGAGTTTTTGCCCAATACTATTCAGGAGCAACTTATGCTTGAAAGGGATCCCCATGGCAATGTTCAGgtaaagattg ... gttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgctgaaaggatatcagtaagctagacatgctaactaggtgttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC
                                 tgctaac  putative branch site (score: 849)
                                              ttatttc  putative PPT
                                            tgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagattgggaatattgtttaaccatcttaacttagtctcttctggcaggactctttctgctgaaaggatatcagtaagctagacatgctaactaggtgttatttcagGTCGCAAAAATTGAAACCGAGAAAATGCTCATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAGGCAGAGGGGAGATACTCTGCACATTTCAGAGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT