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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcgagaactatatttgatattttctggtggacaattgatttctgtcagagtaaaccttgcgctttcaccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 21
gtacactcgagaactatatttgatattttctggtggacaattgatttctgtcagagtaaaccttgcgctttcaccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT
|||  ||| ||| |||  | |||||| ||||  ||  ||  ||||| || |    |||| ||    ||||  |  |||| |||||| ||||||||||| ||||||||||||||| | ||||| |||||||| || || |||||||||||||||||||| || |||||||||||||| ||| ||
gtaatctcaagaccta-gtctgatatattctcttgtgcatatgattgctattgttgtaatccacatgcttctattatttccagGTATTTGTACTTCTTCGAGAAAGGAATTCCAGAGATCACGAACACTGTAATCCAGGATTTGATTGAATTGATTAGGACAGAGAAGCAAAGTGAGAACACT
















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|32865287|gb|CF004969.1|CF004969
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|24768924|gb|CA404053.1|CA404053
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|31356855|gb|CD441212.1|CD441212
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|67012219|gb|CO440968.1|CO440968
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211321315|gb|FL043264.1|FL043264
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|18964320|gb|BM660937.1|BM660937
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|24769517|gb|CA404646.1|CA404646
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211321314|gb|FL043263.1|FL043263
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAY
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|32807352|gb|CD959586.1|CD959586
EST:     GATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: GATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|67014984|gb|CO443733.1|CO443733
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|5846906|gb|AI999989.1|AI999989
EST:     AGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: AGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|32865123|gb|CF004805.1|CF004805
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|148965444|gb|EE016250.2|EE016250
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|6827586|gb|AW331229.1|AW331229
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211321316|gb|FL043265.1|FL043265
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|32806077|gb|CD958311.1|CD958311
EST:     GATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: GATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211462641|gb|FL447919.1|FL447919
EST:     TCAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211321311|gb|FL043260.1|FL043260
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|7162539|gb|AW520161.1|AW520161
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|37382801|gb|CF628365.1|CF628365
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|211321310|gb|FL043259.1|FL043259
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|5296300|gb|AI783070.1|AI783070
EST:     AGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: AGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
EST: gi|32865124|gb|CF004806.1|CF004806
EST:     ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAA                         GTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT
genomic: ACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGAT

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: 268

TGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

TGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TGAAGCGTGCCTTGAGAATCGCAAATGCTGCTCAACAGATGGCTAGTGCTACAAGGGGGAGCAGTGGATCTGTAACCCTATTTATTGAAATTTTGAACAAgtacactcga ... ccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggtggacaattgatttctgtcagagtaaaccttgcgctttcaccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT
          aattgat  putative branch site (score: 268)
                                       ctttcaccattttc  putative PPT
          aattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactcgagaactatatttgatattttctggtggacaattgatttctgtcagagtaaaccttgcgctttcaccattttcagGTACTTGTACTTCTTTGAGAAAGGAATTCCACAAATCACAAACACTGTGATTCAAGATTTGATTGAATTGATTAGAACGGAGAAGCAAAGTGATAACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG