Sequence
atgc intronic sequence ATGC exonic sequencegtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
Basic information
species | Glycine max |
transcript | GLYMA11G36000.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 6
gtacggtt----atcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
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gtaaaatctacaatctttggttatatttgtataacaacatcgccagtttacattctgcttgattcaacattgttgctttagttgatgatgccttt-catctgagtaacattt--tcactca-actatttattattgattaatctgtctaatcccatcatttggtctttctgttgtcagTCATTGGAGATGTTAGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
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---------------------------------------------------------------------------------------------gtaagtaccaaacaaacttatataatcagatcatttactctgtttttacttacaaccgtg------tctgtttggtttcagTCATTGGAGACGTGAGAGGAAGAGGGTTAATGGTTGGGATTGAGCTTGTGAGTGACCGGAAAGACAAGACACCAGCCAAGGCTGAAACATCTGTCTTGTT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 6
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
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--------------------------------------------------------aagttcaaacctttgat---tctgcttcttcctttct--ctgaattgagcattat------ggccagtcat-tttcatggtgttctta--tatct-attaaaccttgtttct---cagTTATCGGAGACGTAAGAGGAAGGGGTCTAATGGTGGGGGTGGAACTTGTGACTGACAGAAAAGAGAAGACCCCTGCCAAAGCAGAAACTGCAGTTTTGTTMapped 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|9820018|gb|BE555531.1|BE555531EST: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACA TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATNTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
EST:
gi|193352675|gb|FK315965.1|FK315965EST: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACA TCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
genomic: TGGTTCTCACTTGATTCAGCGTTTAAGATCCCTGATGCAAATACATGACAgtacggttat ... atatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
ttttgat putative branch site (score: 4)
ataattttgttgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggttatcttgaatcttatataccaaaaagattcatgcttttgtgttgtgatatatttttattttttgatacatttgccttttcttatgtatctatatgaagcttcattacatagaacatacatatgccataattttgttgattattttgataatttttatatatgtccagTCATTGGAGATGTAAGAGGAAGAGGCTTAATGGTGGGGATAGAATTTGTCACCGATAGAAAAGAGAAGACACCTGCAAAGGCTGAAACAACAGCATTGCA
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