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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG

Basic information

species Zea mays
transcript GRMZM5G866758_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaa--ttttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG
|   | ||   || | || ||||| ||| | | | | | ||  ||| |||| ||||||||   |||  |   |||| | |  ||||| | ||||||  ||||||||| | |||||| |||||||| ||||||||||||||||||||  |||||||||||||||||||||||||| |||||
ccggtgatca-cattgatttgttgtaatatttctat-tatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
















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|20300202|gb|BQ163145.1|BQ163145
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18661821|gb|BM501596.1|BM501596
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|22490495|gb|BU050418.1|BU050418
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18450558|gb|BM428836.1|BM428836
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18654813|gb|BM499618.1|BM499618
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|87152006|gb|DY396795.1|DY396795
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|20300665|gb|BQ163608.1|BQ163608
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|211292808|gb|FL187022.1|FL187022
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|19821841|gb|BQ047865.1|BQ047865
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|22490486|gb|BU050409.1|BU050409
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|89106507|gb|DY576724.1|DY576724
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|19770473|gb|BQ035194.1|BQ035194
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|20300437|gb|BQ163380.1|BQ163380
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|19058058|gb|BM736725.1|BM736725
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAAT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT

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: 209

CATGCTTAAGGATGGGCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

CATGCTTAAGGATGGGCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 277

CATGCTTAAGGATGGGCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

CATGCTTAAGGATGGGCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG
                             atttaat  putative branch site (score: 266)
                                   ttttacttattctt  CT-rich tract
     aaatatatttccaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggt