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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattagaaacgtggaccactagtaggcagtactacctggtatcaaatccaattgtccagtagctgatcaatgcttttacaatttgcgagcattccatcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 12
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|76018055|gb|DT945225.1|DT945225
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|211256989|gb|FL181069.1|FL181069
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCCTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|76281862|gb|DV021430.1|DV021430
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|211077349|gb|FK960593.1|FK960593
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACC-CCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|6827926|gb|AW331569.1|AW331569
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCCCCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|211077347|gb|FK960591.1|FK960591
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATC
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATC
EST: gi|32835742|gb|CD975420.1|CD975420
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|33096039|gb|CF056033.1|CF056033
EST:     GCCTGCAAACTCCAAACCAAAACCAAGGGAGTTTGCTCTGAAACCACCAG                         GTCGCCCGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA
EST: gi|37384588|gb|CF629383.1|CF629383
EST:     ACCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAG                         GTCGCACGACATCTACAGGAGGAAGCCAGGCGATAGGAGGATCTTTAGTGA
genomic: GCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGA

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), 49 (downstream exon)
Score: 173

CAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 37

CAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 12

CAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 76

CAGAAGGCCCCATCAAGGATAGCCAGGCTATTCCACACAAAGAATGGACAGCCTGCAAACTCCAAACCAAAACCAAGGGAGTCTGCTCTGAAACCACCAGgtacattaga ... tcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtccagtagctgatcaatgcttttacaatttgcgagcattccatcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT
         agctgat  putative branch site (score: 76)
                                        ttccatc  putative PPT
                      ttttacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattagaaacgtggaccactagtaggcagtactacctggtatcaaatccaattgtccagtagctgatcaatgcttttacaatttgcgagcattccatcatctacagGTCGCACGACATCTACAGGAGGAAGCCAGGCGACAGGAGGATCTTTAGTGAAACCCCCTAAGAGGCGGTAGAGAAATAAAGATTCCATCATCTAGGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG