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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcctatcgcttgccgatcataaatcaatcgcaccttcgcgtcgcgctgctgaatttttaaatttaaagccgggttttttgggtgcgccgagatc...

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 1
CCTGCTCCTTCCCGATCCCCGAGGCAAA----GCTGCGACT-----CCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcctatcgcttgccgat---cataaatcaatcgcaccttcgcgtcgcgctgctgaatttttaaatttaaagccgggttttttgggtgcgccgagatc
         |||||||| |||||||||     || ||  |      | ||  |||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||| ||||||   ||||| ||  |   ||  |    |||   ||  || | || |  || |      |    |       |   ||||| ||| ||  |   | 
---------TCCCGATCTCCGAGGCAAGCAGCGCCGCACCCGGCCGCTGCCGCCGCCGCCATGGCGTTCGAGAAGATCAAGGTCGCCAACCCCATCGTCGAGATGGACGgttagatccc-ccgcttccctctccgcaccagcagatctgtcccgcg-gacgaggcgccgttcgcatgcgctgggttttgatattttttggttcgtgggtgt-
















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|148957374|gb|EC903424.2|EC903424
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211301308|gb|FL411053.1|FL411053
EST:     CATGGSSTTCGAKAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211348619|gb|FL403648.1|FL403648
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211202503|gb|FL419113.1|FL419113
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211245761|gb|FL421854.1|FL421854
EST:     CATGG-STTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211158137|gb|FL392765.1|FL392765
EST:     CATGGSSTTCGANAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         G-GATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211531114|gb|FL426904.1|FL426904
EST:     CATGG-STTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211003472|gb|FL408513.1|FL408513
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|29130876|gb|CB381580.1|CB381580
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211516468|gb|FL412101.1|FL412101
EST:     CATGG-GTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211414079|gb|FL428571.1|FL428571
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211365953|gb|FL391119.1|FL391119
EST:     CATGG-STTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211113009|gb|FL402637.1|FL402637
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211500096|gb|FL423896.1|FL423896
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|50338700|gb|CO533826.1|CO533826
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211214727|gb|FL396531.1|FL396531
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|18659665|gb|BM500459.1|BM500459
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
EST: gi|211352901|gb|FL376492.1|FL376492
EST:     CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACG                         GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG
genomic: CATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG

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: 45 (upstream exon), 48 (downstream exon)
Score: 155

CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 489

CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 716

CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 486

CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcct ... cctattatagGTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTCCTTCCCGATCCCCGAGGCAAAGCTGCGACTCCGCAACCGCCGCCATGGCGTTCGAGAAGATCAAGGTCTCCAACCCAATCGTCGAGATGGACGgtgagatcctatcgcttgccgatcataaatcaatcgcaccttcgcgtcgcgctgctgaatttttaaatttaaagccgggttttttgggtgcgccgagatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA