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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgccaccattttatatttgggccttcaactataactagctccagacttgaagtaaaagtcatatttgattatcgccttcatatgtggttacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT

Basic information

species Zea mays
transcript GRMZM5G898597_T01
intron # 1
splice site 3'
intron type U2

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|44901004|gb|CK827549.1|CK827549
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|211211608|gb|FL139134.1|FL139134
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTCGGTAGGT
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGT
EST: gi|21390351|gb|BQ528400.1|BQ528400
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|32942727|gb|CF047546.1|CF047546
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|37398164|gb|CF636391.1|CF636391
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|211209047|gb|FL139124.1|FL139124
EST:     TCTGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAA
genomic: TC-GAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAA
EST: gi|211447209|gb|FL476655.1|FL476655
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|22935478|gb|BU571753.1|BU571753
EST:     GTCGAGGAGGATGACAACCCTGTCGGCGGTGGCTTCCCGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|5525365|gb|AI861258.1|AI861258
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|22542294|gb|BU092732.1|BU092732
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|21481131|gb|BQ577814.1|BQ577814
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|44900341|gb|CK826886.1|CK826886
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|211211613|gb|FL139139.1|FL139139
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAAYTTGGTAGGTATCCTTTGATTGGACTTCATCAG
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAG
EST: gi|5915554|gb|AW053195.1|AW053195
EST:     GTCGAGGAGGATGACACCACTGTCGGCGGTGGCTAACAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|5455995|gb|AI833685.1|AI833685
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|78022779|gb|DV491166.1|DV491166
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|28984784|gb|BQ539199.2|BQ539199
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|87154268|gb|DY399057.1|DY399057
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|12971520|gb|BG267523.1|BG267523
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTAAAACAAA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|22542416|gb|BU092854.1|BU092854
EST:     GTCGAGGAGGATGACAACCCTGTCGGCGGTGGCTACCCGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|113703370|gb|EE680874.1|EE680874
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|22935479|gb|BU571754.1|BU571754
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|211206465|gb|FL139106.1|FL139106
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|6760490|gb|AW324649.1|AW324649
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|22935554|gb|BU571829.1|BU571829
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
EST: gi|21390572|gb|BQ528621.1|BQ528621
EST:     GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAG                         GAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA
genomic: GTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 68

AGCAGTTCGACCCCACCAATGACTTCCCCGTACCATACGTCAACACCACCGTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

AGCAGTTCGACCCCACCAATGACTTCCCCGTACCATACGTCAACACCACCGTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

AGCAGTTCGACCCCACCAATGACTTCCCCGTACCATACGTCAACACCACCGTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 47

AGCAGTTCGACCCCACCAATGACTTCCCCGTACCATACGTCAACACCACCGTCGAGGAGGATGACAACACTGTCGGCGGTGGCTACCAGAAGTGACTCAGgtgagaggtg ... tacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttgaagtaaaagtcatatttgattatcgccttcatatgtggttacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT
                   atttgat  putative branch site (score: 47)
         taaaagtcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgccaccattttatatttgggccttcaactataactagctccagacttgaagtaaaagtcatatttgattatcgccttcatatgtggttacattgcagGAAAGCTTGCTGGTTAATTTGGTAGGTATCCTTTGATTGGACTTCATCAGAAGCGGCACTATTTTCATTCCAGCTATTAAATATCCCCTTTTCTTTTGTT

- - ccaccat
- - - - - - - - - - - gccttca
- - - - - - - - - - - - - - - - - - - -gctccag
- - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaaa