Sequence
atgc intronic sequence ATGC exonic sequencegtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgcagcagttgtatgatatatccctgttgttgatatgtgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA12G29450.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 5
gtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgcagcagttgtatgatatatccctgt-tgttgatatg-tgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
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--------------------------------------------------------------------gtgcttcccctgctgcattcatcctaacacaattaatttctgtgg-gcttttggttgtgatt-acacaaacttacttt-ctaaagttctcatccag-atttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 5
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 5
gtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgcagcagttgtatgatatatccctgttgttg-atatgtg-tgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
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--------------------------------------------------------------------------------------------gtaaaaaatagtctgctgctctgtatcctttctttgt------aacattttcatgtttgagtgagcggtttaaataaccaaaatgcaatattggtgatgcagATGATACTAATTTTAACAAAATCAATAGACAGATGTTTTGAAAAGAATGCAAAGTTCGATATGACACCCTTGCTTGGAGGGACAGATGCTGTCTTCTCAT
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 5
gtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgca-gcagttgtatgatatatccctgttgttgatatgtgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
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--------------------------------------------------------------------------------------------ctgcttaccgcttaagcattctgcccaattctgtt-ttaacaaaaatattttttgatatttatggtagttctccattcttttgattttgatatggatgcagATGCTACTTATTCTGACAAAGTCAGTAAATAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACCCCTTTGCTCGGAGGAACAGATGTTGTCTTCTCTTMapped 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|9564602|gb|BE474111.1|BE474111EST: AAGAGCCTTATGAGTCACTAAGGGGGCAGTTGGAGCTTATTCATGGTCAG ATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCG
genomic: AAGAGCCTTATGAGTCACTAAGGGGGCAGTTGGAGCTTATTCATGGTCAGgtataactga ... atgtgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagttatgttgcagcagttgtatgatatatccctgttgttgatatgtgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
tgttgat putative branch site (score: 4)
tatgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgcagcagttgtatgatatatccctgttgttgatatgtgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA