Sequence
atgc intronic sequence ATGC exonic sequencegttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 10
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTG-GCTCTATGAATGGAG
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--------------------------------------------------gttagttttaaatctctaccaggaaataattcata--ctatgtgtaggctgtgaaataa-------ccatctgatatt---tagGGCGAGGAAATATGTGTAGCACTTCAGACGCATATCAATGATGTGATGCTCCGCAGATATTCAAAAGCACGCTCTGCTACTAGCGCGGTTTCTCAAAACG-
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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------------------------------------------------gtataatacctttgttgatgttgcacaaactttctttg------gaattattttgtcacactggtattttatctcttggt-tgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTAGTGGTTCTC
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 12
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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-----------------------------------------gtataatacctttgttgatgatgtcacaca---aacccttgttt--ctttggaattattttgcctcactgatattttat-ctatttgttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACATATAAATGATGTAATGCTGCGCCGTTATTCGAAAGCACGATCAGCTGCTGCTGGTGGTGGTTCTCTGA
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatag-agttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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--------------gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 12
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtct--cttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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----------gtattggcatgttcagggacac-tgtactcttcctagttcttaatttcgacctttggacttgactcatatcttcattactt-tgaagttattttattttattggtattttat--cattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGACGTAATGTTGCGACGCTATTCCAAAGCTCGATCTGCTGTGGGTGAATCTTTGAATGAAG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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------------------------------------------------gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtt-tgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 13
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
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-------------------------------------gttattttcgtacctagatcttgctttgtacttgcaaatccctatattatt--ttggagatttatt-tttggt---------ttgtcttgtgagcagGGGGAAGACATTTGCGTAGCACTTCAGACACACATTAATGATGTTATGTTGCGGCGATACTCCAGAAACAAAAATATTCCTAATGGGCAGGTATCAAATGMapped 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|34546513|gb|CF514745.1|CF514745EST: AGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAG GGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTG
genomic: AGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgttcttaatc ... ttttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTG
EST:
gi|34544452|gb|CF512684.1|CF512684EST: AGACCATAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAG GGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTG
genomic: AGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgttcttaatc ... ttttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
atttgat putative branch site (score: 5)
ttctattccatttt putative PPT
aaaaaattattatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT