Sequence
atgc intronic sequence ATGC exonic sequencegtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggtaactagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
Basic information
species | Glycine max |
transcript | GLYMA02G44660.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g17390.1 (Oryza sativa), 3'ss of exon 1
gtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggtaactagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
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----------------------------------ctagatgagctcatttgtgtttctttaggatctt--atcttcaaactt-ttagttatgtttgagcaaccggaac---caatcttgaggctttt-------------tgtttgtttgcagCATGGGCATGTTGGATTCATGATGTCATGCTACGATGCAGAGCTCAGCTATGATTTCCACAGTGATACCTTCCGTGCAAG
upper sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggta-actagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
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----------------------------------------------------------gtaatcatttcataaacatagttgctccatttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaaga---------gcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG
upper sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G26850.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggt--aactagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
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----------------------------------------gtaatcatagatttcataaacatat-----atagctactccattttattctttatgggtttgactaaagtag----tgagggcttttttggtgtaaga-------------gcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCTGAGCTCAGCTATGACACTGACACTAATACTTTTCAAGCTAG
upper sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
---------gtatcaa-tcatcatgaacccctttgtgctt-ttttcctattgaaaacttatattctatcatg--ctaccttcaatagtgaaacaaattagttttttcatggtaactagaatagacgattattgtgtttttctcacaagttacatttttcact-gcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
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gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAGMapped 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|14259413|gb|BG882321.1|BG882321EST: CTCTTGAGACTGGCAATTTCTGGTTTCCTGCTCAGGTCTATAACCGTGAG AATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTAT
genomic: CTCTTGAGACTGGCAATTTCTGGTTTCCTGCTCAGGTCTATAACCGTGAGgtatcaatca ... ttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTAT
EST:
gi|6482324|gb|AW201591.1|AW201591EST: CTCTTGAGACTGGCAATTTCTGGGTTCCTGCTCAGGTCTATAACCGTGAG AATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTAT
genomic: CTCTTGAGACTGGCAATTTCTGGTTTCCTGCTCAGGTCTATAACCGTGAGgtatcaatca ... ttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
ttctcac putative branch site (score: 2)
tttttcact putative PPT
attattgtgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaatcatcatgaacccctttgtgcttttttcctattgaaaacttatattctatcatgctaccttcaatagtgaaacaaattagttttttcatggtaactagaatagacgattattgtgtttttctcacaagttacatttttcactgcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT