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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacaaagttgatatgcaacatttatattcttgtggaagcatcgctatgttttttgcctagagagtttcttgacgatctgtgtgccaccgatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT

Basic information

species Zea mays
transcript GRMZM2G116053_T01
intron # 7
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|32909197|gb|CF014009.1|CF014009
EST:     TAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGGCCGTTCAG                         GCAAA-GTTTTTGTAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTG
genomic: TAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAA-GCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTG-AATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTG
EST: gi|44901544|gb|CK828089.1|CK828089
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|60358629|gb|DN225602.1|DN225602
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|22545435|gb|BU097794.1|BU097794
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|148930001|gb|EE285859.2|EE285859
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|87157609|gb|DY402398.1|DY402398
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|71309820|gb|DR791192.1|DR791192
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|21843373|gb|BQ703954.1|BQ703954
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATTTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|211334852|gb|FL189644.1|FL189644
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|211291293|gb|FL447806.1|FL447806
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|71758676|gb|DR956613.1|DR956613
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|211334851|gb|FL189643.1|FL189643
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|37401792|gb|CF638264.1|CF638264
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|22935601|gb|BU571876.1|BU571876
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|148952884|gb|EC898876.2|EC898876
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|149110497|gb|EE294157.2|EE294157
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|87156744|gb|DY401533.1|DY401533
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
EST: gi|60401205|gb|DN234012.1|DN234012
EST:     CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAG                         GCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC
genomic: CTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCC

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: 66

TGGGATCCTAATCGCGGTAATCGGGATGGTTCTGTACTCGTACTTCTGCACTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

TGGGATCCTAATCGCGGTAATCGGGATGGTTCTGTACTCGTACTTCTGCACTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 145

TGGGATCCTAATCGCGGTAATCGGGATGGTTCTGTACTCGTACTTCTGCACTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

TGGGATCCTAATCGCGGTAATCGGGATGGTTCTGTACTCGTACTTCTGCACTAGAGAGACTCAGCAAAAACCAGCAGAAGCCTCCCCGCAAGCCGTTCAGgtatgttctg ... gatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgttttttgcctagagagtttcttgacgatctgtgtgccaccgatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT
                       tcttgac  putative branch site (score: 69)
     tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacaaagttgatatgcaacatttatattcttgtggaagcatcgctatgttttttgcctagagagtttcttgacgatctgtgtgccaccgatatcgcagGCAAAGGAGGGTGAATCGAACCCGCTGATCTCGGACTCCCTGAGCGCTGCCGAAAATGGAGGCAGTGCCACCGACGATGAACCTCTGAAGGTACCAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - -tatgcaa
- - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgccac