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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtagcggcagcttcagttcgacacatcttgctgttttcgattgtttattcaccccgcatgaggtaaattcttctttggtgggtatgccaaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG

Basic information

species Zea mays
transcript GRMZM2G173321_T02
intron # 4
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|26456740|gb|CA828323.1|CA828323
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|76936192|gb|DV174627.1|DV174627
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCTCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|78074656|gb|DV503090.1|DV503090
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|149051910|gb|EE156043.2|EE156043
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|78093455|gb|DV521829.1|DV521829
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|26457345|gb|CA828928.1|CA828928
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|78544304|gb|DV621802.1|DV621802
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|60345741|gb|DN212714.1|DN212714
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|71333334|gb|DR803728.1|DR803728
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|60397540|gb|DN230356.1|DN230356
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|93281470|gb|EB673734.1|EB673734
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|211139833|gb|FL206379.1|FL206379
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGC-TCC-AAATCA
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCA
EST: gi|211138902|gb|FL206375.1|FL206375
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGT
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGT
EST: gi|20507484|gb|BQ279652.1|BQ279652
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|71333335|gb|DR803729.1|DR803729
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|78544746|gb|DV622244.1|DV622244
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
EST: gi|213170597|gb|FM195452.1|FM195452
EST:     TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTG                         GGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG
genomic: TCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACG

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), 32 (downstream exon)
Score: 80

CATCTGTAAGGCGGAGGAAGTGGAGCAAGAGCTGGACTCCAGCTTCCCCGTCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 20

CATCTGTAAGGCGGAGGAAGTGGAGCAAGAGCTGGACTCCAGCTTCCCCGTCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 18

CATCTGTAAGGCGGAGGAAGTGGAGCAAGAGCTGGACTCCAGCTTCCCCGTCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 10

CATCTGTAAGGCGGAGGAAGTGGAGCAAGAGCTGGACTCCAGCTTCCCCGTCTTCATCAAACCCATGACCCAGTCCCATGTCACCGGAGGCTTCTGGCTGgtaaagtagc ... caaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattcaccccgcatgaggtaaattcttctttggtgggtatgccaaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG
                     taaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtagcggcagcttcagttcgacacatcttgctgttttcgattgtttattcaccccgcatgaggtaaattcttctttggtgggtatgccaaaccgcagGGCCTCCCAAATCATTTCTGCCGGAAGTACCTGCCCAAGCGTGACGAGACGATCACCCTGCTGGATGAGGATGACAACGAGTCCTACACGCTATACCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG