Sequence
atgc intronic sequence ATGC exonic sequence...ggattcaaattcacttcatcttgcatctcatggattctctcaggaatatgccaccatgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 6
ggattcaaattcacttcatcttgcatc--tcatggattctctcaggaatatgccaccatgcccat--caatctcat--gacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
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--gtataagttcaacgaactccatatgcattatttcttgtctaaagaatatgctcacctgaacatgttgatctgactggataagcttcctttggat----ctgcagATAAGTTTAGATCAGATCTCATGAACATTGCCATGACTACACTTAGTTCAAAAATCCTCTCTCAGGACAAGGAGTACTTTGCTGAACTTGCTGTTGATGC
upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
ggattcaaatt---cacttcatcttgcatctcatggattctctcaggaatatgccacca-tgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
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ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatg--aataatttttctggttaat--gcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
lower sequence: EFJ28920 (Selaginella moellendorffii), 3'ss of exon 6
ggattcaaattcacttcatcttgcatctcatggattctctcaggaatatgccaccatgcccatcaatctcatgacaatattctttttcat-tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
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---------------------------------------------gtctgttggcac-tgcttcaatgtttagagctcagtcttgtgtttgtccattgcagAAAAGTTTCGACAAGATCTTATCAATATTGCTATGACAACTCTGAGTTCAAAAATTCTTTCTCAGGAGAAAGAACATTTTGCCAATCTTGCTGTGAATGC
upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
lower sequence: EFJ13624 (Selaginella moellendorffii), 3'ss of exon 6
ggattcaaattcacttcatcttgcatctcatggattctctcaggaatatgccaccatgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
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---------------------------------------------gtctgttggcactgcttcaatttttagagctcagtcttgtgtttgtccattgcagAAAAGTTTCGACAAGATCTTATCAATATTGCTATGACAACTCTAAGTTCAAAAATTCTTTCTCAGGAGAAAGAACATTTTGCCAATCTTGCTGTGAATGCMapped 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|18385234|gb|BM418433.1|BM418433EST: TGCCAGAGATTCTTTGCTAAAAAAGNCCATGGCCAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTACTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|18384285|gb|BM417484.1|BM417484EST: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTACTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|19821794|gb|BQ047818.1|BQ047818EST: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTACTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|22819752|gb|BU499842.1|BU499842EST: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|17970295|gb|BM277058.1|BM277058EST: CCAGGAGAATCTTTGGCTAAAAAGGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTACTATGACTACTCTTAGTTCAA
genomic: CCA-GAGATTCTTT-GCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|14191163|gb|BG833393.1|BG833393EST: TGCCAGACATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTGCTATGAC
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGAC
EST:
gi|87152447|gb|DY397236.1|DY397236EST: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAG ATAAATTCAGATCTGATCTCATGAATATTACTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|19822007|gb|BQ048031.1|BQ048031EST: AAAAGACCATGGACAACAAAGAAAATACAG ATAAATCCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
genomic: AAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
EST:
gi|18384286|gb|BM417485.1|BM417485EST: TGCCAGAGATTCTTTGCTAAAAAAGNCCATGGCCACCAAAGAAAATTCAG ATAAATTCAGATCTGATCTCATGAATATTCCTATGACTACTCTTAGTTCAA
genomic: TGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAA
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:
347GTTACAGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
199GTTACAGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
141GTTACAGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
169GTTACAGAATGGCTCTCGAGTGTGCCAGAGATTCTTTGCTAAAAAAGACCATGGACAACAAAGAAAATACAGgtaagttatt ... tcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgccaccatgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
tattctttttcattct CT-rich tract
aatattctttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattcaaattcacttcatcttgcatctcatggattctctcaggaatatgccaccatgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - -cacttca
- - - - - - - - - tcttgca
- - - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - ccaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaca