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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatggagtggccccttcaatcatagatttgtacgatatagaatccagcattccagcgatgacaagtttttaagtggtactaacagtttgcgcaggttgttttgtgttattcatgttttaacaagtgagtggtcaactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 7
gtaagtgatggagtggccccttcaatcatagatttgtacgatatagaatccagcattccagcgatgacaagtttttaagtggtactaacagtttgcgcaggttgttttgtgttattcatgttttaacaagtgagtggtcaactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG
                                             || |||      ||||  |  |  ||||||         | |   |  || ||   |   | ||| |||| || | | |||||  | ||   |||  ||||||| ||||||| || ||  |||||||| ||| |||| |||||||| |||||||||| || | || ||||||||||||||||||| |||| ||||| |||||||
---------------------------------------------gagtcctcaccaccag-aaccatgagttttaccactaggccacgtgaatgtgcccatc--tctgttttatgcaagatataacatattagcattca-ttattcagGTTGAAGAAGACCTGAAAAATGGAATTGTTGGGTCTGTTCCAATTCCACCTGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTG
















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|5915132|gb|AW052773.1|AW052773
EST:     CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|6031340|gb|AW076197.1|AW076197
EST:     CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|26457260|gb|CA828843.1|CA828843
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACGAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|32830978|gb|CD970656.1|CD970656
EST:     ATTTGA-TTTGAAGAAACTAAAGAAGACATC-AACTATTTGCGCATCC-A                         ATTGAAGATGATCTACAAAATGGAGTTGCT-GGGCTGTTCCAGTTCCACCC
genomic: ATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTA-TTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCA-CC
EST: gi|32828287|gb|CD967965.1|CD967965
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|21390180|gb|BQ528229.1|BQ528229
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACGAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|7216517|gb|AW562639.1|AW562639
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACGAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|32858009|gb|CD997690.1|CD997690
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|31355926|gb|CD440283.1|CD440283
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACGAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|5847181|gb|AW000260.1|AW000260
EST:     CATTTGACTTTGAGGAAACTAAA-AAGAC-TCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|32830644|gb|CD970322.1|CD970322
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|31356801|gb|CD441158.1|CD441158
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACGAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|5915112|gb|AW052753.1|AW052753
EST:     CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|32831486|gb|CD971164.1|CD971164
EST:     CATTTGATTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
EST: gi|5343257|gb|AI795562.1|AI795562
EST:     CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAA                         ATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT
genomic: CATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCT

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: 277

TGTCATGTTCCCTTATGCTCGTGATAATGTACGAAAACATCTGACTTCTACATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 422

TGTCATGTTCCCTTATGCTCGTGATAATGTACGAAAACATCTGACTTCTACATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 846

TGTCATGTTCCCTTATGCTCGTGATAATGTACGAAAACATCTGACTTCTACATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

TGTCATGTTCCCTTATGCTCGTGATAATGTACGAAAACATCTGACTTCTACATTTGACTTTGAGGAAACTAAAGAAGACATCAAACTATTGCGCATCCAAgtaagtgatg ... aactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcaggttgttttgtgttattcatgttttaacaagtgagtggtcaactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG
                          ttttaac  putative branch site (score: 213)
                 ttattcatgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgatggagtggccccttcaatcatagatttgtacgatatagaatccagcattccagcgatgacaagtttttaagtggtactaacagtttgcgcaggttgttttgtgttattcatgttttaacaagtgagtggtcaactattcagATTGAAGATGATCTACAAAATGGAGTTGCTGGGGCTGTTCCAGTTCCACCTGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG