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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacaacatgcaaaatgcaattgtttgttagtctgcagtattactccatggtaatatcgtccttaatacatataatgaacctaatgtttatctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA

Basic information

species Zea mays
transcript GRMZM2G138349_T03
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|60672574|gb|DN475276.1|DN475276
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211169837|gb|FK962697.1|FK962697
EST:     GCGTWAAATGTTCTGGCGTCCATAGAAGYCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCAT
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCAT
EST: gi|211166491|gb|FK962680.1|FK962680
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211169840|gb|FK962700.1|FK962700
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAG
EST: gi|211168166|gb|FK962693.1|FK962693
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168168|gb|FK962695.1|FK962695
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168157|gb|FK962684.1|FK962684
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168159|gb|FK962686.1|FK962686
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTTGACTCCAT
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTT-GACTCCAT
EST: gi|71768791|gb|DR966728.1|DR966728
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211169838|gb|FK962698.1|FK962698
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168160|gb|FK962687.1|FK962687
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168169|gb|FK962696.1|FK962696
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168161|gb|FK962688.1|FK962688
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACA
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACA
EST: gi|211168164|gb|FK962691.1|FK962691
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGT
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGT
EST: gi|211168167|gb|FK962694.1|FK962694
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168165|gb|FK962692.1|FK962692
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|31250107|gb|CD219131.1|CD219131
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GNTCTGTCAGTGACACTGGNACAAGTGGTCTGACNGTGAAGTTGACTCCAT
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGG-ACAAGTGGTCTGACAGTGAAGTTGACTCCAT
EST: gi|211168163|gb|FK962690.1|FK962690
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|50334443|gb|CO529569.1|CO529569
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|78087464|gb|DV515857.1|DV515857
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATG
EST: gi|211168156|gb|FK962683.1|FK962683
EST:     GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG                         GTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATT
genomic: GCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCAT-

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: 43 (upstream exon), 49 (downstream exon)
Score: 42

ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 73

ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAGgtttttgtag ... tctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatggtaatatcgtccttaatacatataatgaacctaatgtttatctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA
                                            atctgac  putative branch site (score: 73)
                                         tttatct  CT-rich tract
                 ttaatacatataatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacaacatgcaaaatgcaattgtttgttagtctgcagtattactccatggtaatatcgtccttaatacatataatgaacctaatgtttatctgacacagGTTCTGTCAGTGACACTGGACAAGTGGTCTGACAGTGAAGTTGACTCCATGATAGAAGTTGGTGGGAATTCTCAGGCAAACGCAATATATGAGGCTTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - -acatgca
- - - - - - -aatgcaa
- - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - -tctgcag
- - - - - - - - - - - - - - - - - - - - - -ctccatg