Sequence
atgc intronic sequence ATGC exonic sequencegttcatactttccatcggccatcaccctattctttaaaagtagtgtgttcttgatcttgttaaactctaaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 4
--gttcatactttccatcggccatcaccctattctttaaaagtagtgtgttcttgatcttgttaaactctaaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
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agggcctaacattaaaagaaaaaaaacttcattttgcagataaaatgt-tgaaagatgcatctatact----gttttctaccttaatttgatcctatctg----tgcagGAAGAATGTGAAAAAGTTGCCAGAAGTGAGGCATTAGCCATCCGGTTATCTAATATAGCAAACATGGTTCTTTTTGCTGCAAAAGTTTATGCCTCAATAA
upper sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G52280.1 (Glycine max), 3'ss of exon 2
gttcatactttccatcggccatcaccctattctttaaaagtagtgtgttcttgatcttgttaaactct-aaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
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--------------------gtttctttttctcttttatggtctctagatttaagattgatatgtagtcaaatgcttttg-ctgaatatccactgatgtgg---gcagGAAGAGCGAGACAAGTTAGCAAGAAGTGAGACATTTGCCATCAGAGTGTCAAATGCAGCAAACATGGTTCTTTTTGTTGCCAAAGTTTATGCATCAATCA
upper sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtt--catactttccatcggccatcaccctattctttaaaagtagtgtgttcttgatcttgttaaactctaaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
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gttagcctaaatgaggctactacttgtcacatttgttgaaaccatgatgcatttgttcttgttgattgatacttttctgaatttctttg----tgttttgtgtacatagGAAGAGCAGGATAATTTGGCTAAAAGCGAGACATTGGCGATTAGAATATCAAACATTGCAAACATGCTTCTTTTTGCTGCTAAAGTCTATGCTTCTGTCAMapped 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|110712799|gb|EE088171.1|EE088171EST: ATGAAATGGACGCCTTGGCAGATCATGGATATATTCCTCGAATGACAGAG GAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCA
genomic: ATGAAATGGATGCCTTGGCAGAGCATGGATATATTCCTCGAATGACAGAGgttcatactt ... gggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCA
EST:
gi|110711822|gb|EE088743.1|EE088743EST: ATGAAATGGACGCCTTGGCAGATCATGGATATATTCCTCGAATGACAGAG GAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCA
genomic: ATGAAATGGATGCCTTGGCAGAGCATGGATATATTCCTCGAATGACAGAGgttcatactt ... gggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcttgttaaactctaaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
gactaaa putative branch site (score: 2)
taattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatactttccatcggccatcaccctattctttaaaagtagtgtgttcttgatcttgttaaactctaaatgcctcagactaaatggtaattgtttgggtttgcagGAGGAAAGGGAAAAGTTGGCTCGAAGTGAGACAACTGCCATTAGAATATCAAATATTGCAAACATGATTCTTTTTGCTGCTAAGGTTTATGCATCCGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT