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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactcctgtcattcattgccttaacgaatcttattgtccaaagccgtttgtcatcaatctatgctgtaacatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG

Basic information

species Zea mays
transcript GRMZM2G475867_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 18
gtgagactcctgtcattcattgccttaacgaatcttattg-tccaaagccgtttgtcatcaatctatgctgtaacat-atgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG
|| ||| |       |||||   | | || | |||| ||| |||||| ||   ||| || ||| |||  | |||| | |||||||||||||| || |||||||||| |||||||||||| || ||||||||||| |||||||| ||||||||||||||||||
gtaagattttcactgttcatcatcattaccagtcttgttgatccaaaaccacatgttattaatatat-ttataactttatgcagGAATATCTTCAGCGAGAAAGGCTAGGGTCTGCTCGACTAGAGAATTTTGCATCTGCACTTGAACTGATTGGACAAAAG
















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|32924251|gb|CF029063.1|CF029063
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCG
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCG
EST: gi|32924522|gb|CF029334.1|CF029334
EST:     GCTTTCTAAACTCG-CTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: GCTTTCTAAACTCGTC-GCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924638|gb|CF029450.1|CF029450
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924314|gb|CF029126.1|CF029126
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32848274|gb|CD987955.1|CD987955
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924177|gb|CF028989.1|CF028989
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924022|gb|CF028834.1|CF028834
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924179|gb|CF028991.1|CF028991
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTCCACCGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924558|gb|CF029370.1|CF029370
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923896|gb|CF028708.1|CF028708
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923795|gb|CF028607.1|CF028607
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCATGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924605|gb|CF029417.1|CF029417
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924330|gb|CF029142.1|CF029142
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923682|gb|CF028494.1|CF028494
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924338|gb|CF029150.1|CF029150
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|9952966|gb|BE639549.1|BE639549
EST:     AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924097|gb|CF028909.1|CF028909
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923641|gb|CF028453.1|CF028453
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924376|gb|CF029188.1|CF029188
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924146|gb|CF028958.1|CF028958
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923916|gb|CF028728.1|CF028728
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923936|gb|CF028748.1|CF028748
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|56462016|gb|CK986314.1|CK986314
EST:     AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32923696|gb|CF028508.1|CF028508
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
EST: gi|32924087|gb|CF028899.1|CF028899
EST:     AGCTTTCTAAACTCGTTGCTTTTGTCAAGGGGACTCAATTTGATCTTGTG                         GAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT
genomic: AGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCT

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: 62

TGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 44

TGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 63

TGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

TGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTCGTCGCTTTTGTCAAGGGGACTCAATTTGATCTTGTGgtgagactcc ... acatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgaatcttattgtccaaagccgtttgtcatcaatctatgctgtaacatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG
                                        ctgtaac  putative branch site (score: 72)
                                           taacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactcctgtcattcattgccttaacgaatcttattgtccaaagccgtttgtcatcaatctatgctgtaacatatgcagGAATATCTACAACGAGAAAGGCAAGGGTCTGCTCGTCTGGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA