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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatccattcttctacccttcttttaggcattggagtatataatcttgttgtgcttacaaagcatatgagttctcaattccaatcgtgcatgtgcat...

Basic information

species Zea mays
transcript GRMZM2G100794_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 5'ss of exon 2
AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgta---aaatccattcttctacccttctttta--ggcattggagtatataatcttgttgtgcttacaaagcatatgagttct-caattccaatcgtgcatgtgcat
||||||| |||| || ||||| ||||| |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||  | ||| |||||    || | |||||| ||||||| ||||     |||| ||||||||  |    | |   | |       ||  | || | ||| |  | |   | |       
AGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTTGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGATCGTAAGATGgtacactaaactattcttgtaccctttttttttccacattagagtatatttttcattagcattaatgtcttctacaatttttacaaatatagtgtggtaa------

upper sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 5'ss of exon 2
AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatccattcttctacccttcttttaggcattggagtatataatcttgttgtgcttacaaagcatatgagttctcaattccaatcgtgcatgtgcat---
 |||||  | || || |||||||| || ||||| |||||||||||  | || ||||||||||||||||| ||||| ||||||||  || | ||||| |||||||  |   || | |  |   | || |  |  ||||   |  |  | ||| |      ||   ||  |  |||| |   || ||  | || |  | ||    
TGAGCGGATAGGAGAGCCAGACTGCAGTTATTATATGAGGACTGGACTATGTAGGTTTGGGATGACCTGCAAATTCAATCACCCCCCAAATAGAAAACTGgtaatgttacttgtgcatcatgtattatttgt-ttgggtaaagtctttttgatccttgaactttgctca-aagttttttttttcacccctgaa-atacaatac
















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|71439755|gb|DR820805.1|DR820805
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|149000507|gb|EE037687.2|EE037687
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|148938171|gb|EC882453.2|EC882453
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|211078940|gb|FL257763.1|FL257763
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|149083012|gb|EE172259.2|EE172259
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|71772125|gb|DR970062.1|DR970062
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|78089927|gb|DV518301.1|DV518301
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|148944209|gb|EC889301.2|EC889301
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|211078942|gb|FL257765.1|FL257765
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAAGTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|211303560|gb|FL306497.1|FL306497
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|71765018|gb|DR962955.1|DR962955
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|148959485|gb|EC905484.2|EC905484
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|148946035|gb|EC891334.2|EC891334
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|71315475|gb|DR794342.1|DR794342
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|78086204|gb|DV514597.1|DV514597
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
EST: gi|8367349|gb|BE050294.1|BE050294
EST:     GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTG                         GCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG
genomic: GCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAG

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: 33

AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAGCCTGAATGTCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 31

AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAGCCTGAATGTCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 44

AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAGCCTGAATGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatcca ... tgactattagGCTGTTGCTGCTGCAAGAATGAAGGGAGAATATCCTCAAAGAATTGGACAGCCTGAATGTCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGACTGGCATGTGCAGGTTTGGGATGACCTGTAAATTTAATCACCCAGCAGACAGAAAGCTGgtaaaatccattcttctacccttcttttaggcattggagtatataatcttgttgtgcttacaaagcatatgagttctcaattccaatcgtgcatgtgcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG