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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatacctcatgtgttccgagtcatcagattaaactgctttacttgctcctatttttttgcctgatttcattaggcatttaggctagatgatgacaacatatttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 3'ss of exon 2
gtaatcaatacctcatgtgttccgagtcatcagattaaactgctttacttgctcctatttttttgcctgatttcattaggcatttaggctagat---gatgacaa-catatttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG
||||| ||||  ||   |  || | ||  |  |||||| ||| | ||||||||  | ||||| ||  |  || |  |     | | |  || ||   | |||||| | | ||| |||||||||||| | |||||| |||| |||||||| ||||||||||| |||||  | || |||||||| |||||||||||||||||||| ||||||||||||||||
gtaatgaatatatctccttatctgtgttgt--gattaatctgatgtacttgctaatttttttgtgtgtttttcctgtttttctcttgtatatattaagctgacaatcttgtttatttcagCTTATCTTTCCATTTTTGGATCTGGACATTAAGTACTATGACTTGGGAGTTCTCCACCGTGATGCAACTGATGACAAGGTCACCGTGGAGGCTGCAGAGG
















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

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: 226

GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAGgtaatcaata ... tttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 731

GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAGgtaatcaata ... tttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 838

GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAGgtaatcaata ... tttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 769

GTGATGAGATGACCAGGGTATTCTGGCAGTCTATCAAGGACAAGgtaatcaata ... tttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcctgatttcattaggcatttaggctagatgatgacaacatatttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG
   gcctgat  putative branch site (score: 769)
                                           tatttttttc  putative PPT
                                     acaacatattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaatacctcatgtgttccgagtcatcagattaaactgctttacttgctcctatttttttgcctgatttcattaggcatttaggctagatgatgacaacatatttttttcagCTTATCCTCCCATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG