Sequence
atgc intronic sequence ATGC exonic sequencegttggtagtgtatatagagaaacacaacttttcaagttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
Basic information
species | Glycine max |
transcript | GLYMA04G37370.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 3
gttggtagtgtatatagagaaacacaacttttcaagttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
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-------gtgggtgaagtcccaaacactatctctggtcccttgtttgcacttctcttgattttcctgagaatg--tatcacttcattccagGTAAGTTCAGACATTTACCTGTCGTGGAGAACGGTGAAGTCATTGCACTGCTCGACATAGCCAAGTGCCTGTATGATGCTATTGCGCGAATGGAAAGGGC
upper sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
gttggtagtgtatatagagaaacacaacttttcaagttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
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---------gtttgttatttcttgttcttttataagtt-----ctttgttg-gtcttggtacttgagc---tgactagtggatat--gcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
upper sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
-----gttggtagtgtata---tagagaaacacaacttttcaagttagttacttt-tctgtatcctgccttttga-atacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
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gtttgtctcattgtttttaagctagagaaacttgatgttt--atctgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactg-cagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
upper sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
---gttggtagtgtatatagagaaacacaacttttcaagttagt-tacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
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gttgctgataacctgaa-aaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgat---tttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGCMapped 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|15000401|gb|BI321215.1|BI321215EST: TGTTCTTTCTGAAACTCTTGCTGCAGAAGCCCTCCAAAAGATGGTGCAAG GGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAAGTTT-GGCTTTA
genomic: TGTTCTTTCTGAAACTCTTGCTGCAGAAGCCCTCCAAAAGATGGTGCAAGgttggtagtg ... atgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAA-GTTTTGGCTTTA
EST:
gi|11412897|gb|BF424908.1|BF424908EST: TGTTCTTTCTGAAACTCTTGCTGCAGAAGCCCTCCAAAAGATGGTGCAAG GGAAATTCAGACATTTACCTGTGGTGGAGAA
genomic: TGTTCTTTCTGAAACTCTTGCTGCAGAAGCCCTCCAAAAGATGGTGCAAGgttggtagtg ... atgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
ggctgat putative branch site (score: 4)
ttttgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtagtgtatatagagaaacacaacttttcaagttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG