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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaacatagtttgcattcttctctgcgaatatgaagcgtgaacttggtgcagctcctgcaagcaatagctcgttttaactgaacgcagagaaca...

Basic information

species Zea mays
transcript GRMZM2G078839_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078839_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g12260.1 (Oryza sativa), 5'ss of exon 3
TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaacatagtttgcattc--ttctctgcgaatatgaagcgtgaacttggtgcagctcctgcaagcaatagctcgttttaactgaacgcagagaaca
||| |  |    |||||||||| ||||| ||||||||||||||| |||||   |||||||||     |||||||| || || | || | ||||||||||||| || | |      |||||||    |  | || |    ||  || |    ||     |   |  |  |      ||   ||  || || ||  |   | ||
TTTAGCGATGTCTATGTTGGAGGCAGCAGGGAAAGAGCTACTGTACATAACCCGAGATCACCATGTATACAAGAATCTTCTTAGGATATTTATTGTTCAGgtcagtaaagttatttttgcatctggtaatttgtggtcctgctgcattcttttttccaacaacacgtcaatgcatgcaatttccaa-tgcac-taacaagca
















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|32798649|gb|CD950885.1|CD950885
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211525105|gb|FL426868.1|FL426868
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|37401003|gb|CF637863.1|CF637863
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGATGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|91051896|gb|EB162314.1|EB162314
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|31998532|gb|CD662122.1|CD662122
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGA
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGA
EST: gi|32932813|gb|CF037625.1|CF037625
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211317448|gb|FL406235.1|FL406235
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGATCCAGCTGTGCTTCTCCGCTGCAGGGAAG-A
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGG-AAGGA
EST: gi|37379237|gb|CF626354.1|CF626354
EST:     CCCCACTTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGATGCAGGAAGGAG
genomic: CCCCAC-TTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211390321|gb|FL404127.1|FL404127
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|149106149|gb|EE291827.2|EE291827
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|29946371|gb|CB816117.1|CB816117
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|71443317|gb|DR824367.1|DR824367
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|4753442|gb|AI657352.1|AI657352
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|76016568|gb|DT943738.1|DT943738
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211514323|gb|FL422105.1|FL422105
EST:     GTAGAGATCANCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAR
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211054870|gb|FL422547.1|FL422547
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAAACCAGCTGTGCTTCTCCGCTGCA
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAA-CCAGCTGTGCTTCTCCGCTGCA
EST: gi|31911224|gb|CD651817.1|CD651817
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|33467615|gb|CF244664.1|CF244664
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211426054|gb|FL384928.1|FL384928
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTG
EST: gi|211150053|gb|FL377210.1|FL377210
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|74234972|gb|DT642886.1|DT642886
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|15426680|gb|BI542502.1|BI542502
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|29947123|gb|CB816493.1|CB816493
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|29947032|gb|CB816448.1|CB816448
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211082966|gb|FL420019.1|FL420019
EST:     GTAGAGATCACCTCATTTACAAAAAACTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGATGCA
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCA
EST: gi|211518312|gb|FL387236.1|FL387236
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCT
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCT
EST: gi|94479251|gb|EB708209.1|EB708209
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTTTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|211162713|gb|FL378614.1|FL378614
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|15426825|gb|BI542647.1|BI542647
EST:     GTAGAGATCACCCCACTTACAAGGAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|71443402|gb|DR824452.1|DR824452
EST:     GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG
EST: gi|4388055|gb|AI491227.1|AI491227
EST:     GTAGAGATCACCCCNCTTACAAGAAGCTCCTCAAGACACTTATTGTTCAG                         AGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTTTCCGCTGCAGGAAGGAG
genomic: GTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAG

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: 246

TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAGGATCTTCAACTTGTTGATTTAGTTTTGGAATCTGCAAGGAATGAGTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 401

TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAGGATCTTCAACTTGTTGATTTAGTTTTGGAATCTGCAAGGAATGAGTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 288

TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAGGATCTTCAACTTGTTGATTTAGTTTTGGAATCTGCAAGGAATGAGTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaa ... atctgaacagAGTTTGCTGCGCCTGAAAGAACCAGCTGTGCTTCTCCGCTGCAGGAAGGAGGATCTTCAACTTGTTGATTTAGTTTTGGAATCTGCAAGGAATGAGTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGTAACAGATATGTTGGAGTCAGCAAGGAAAGAGCTACTGTGCATAAGTAGAGATCACCCCACTTACAAGAAGCTCCTCAAGACACTTATTGTTCAGgtaagcagaacatagtttgcattcttctctgcgaatatgaagcgtgaacttggtgcagctcctgcaagcaatagctcgttttaactgaacgcagagaaca

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC