Sequence
atgc intronic sequence ATGC exonic sequence...attaatccaattcgatttagaaagacagattgctgaagttgcattttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
Basic information
species | Glycine max |
transcript | GLYMA08G20670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
attaatccaattcgatttagaaagacagattgctgaagttgcattt-taaaatttctttattctgctggtcatc--tgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
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--cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatagtgttaagggattaccatctgcctt-ttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 5
--attaatccaattcgatttagaaagacagattgctgaagttgcattttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
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ttagtggtctacattgatat-gccagttactttcattaatctgtgcaatataaattttgattattgttttacgtgatgccaaaccttatctgtta-gttcagATTCGTCCAGATCGCCAAACACTTTACTGGAGTGCTACCTGGCCGAAGGAAGTTGAGCAGCTAGCAAGGAATTTCCTTTTTGACCCATACAAG
upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
attaatccaattcgatttagaaagacagattgctgaagttgcattttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
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---------gttcg-tttacttactc---ctgtcttcgtcatatatatgtgtatgctagttgctttgtctat---aacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 5
attaatccaattcgatttagaaagacagattgctgaagttgcattt--taaaatttctttattctgctggtcatctgatcactttttttt----tgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
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----atccggcttacctttctcct-ctcttccttgtaattgtatctgttgaattctgcataatctggagat-atcaggttcctatttattggtttgctttatgtagATTCGTCCTGATCGTCAAACCCTCTATTGGAGTGCTACATGGCCCAAGGAGGTGGAACAACTTGCTAGGAAGTTCCTTTACAACCCATGTAAAMapped 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|208183561|gb|GD985311.1|GD985311EST: GGATGTTGGATATGGGGTTTGATCCTCAGCTACGGAAGATTGTCTCTCAG ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAG
genomic: GGATGTTGGATATGGGGTTTGATCCTCAGCTACGGAAGATTGTCTCTCAGgttggcttta ... ttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAG
EST:
gi|15204508|gb|BI427276.1|BI427276EST: GGATGTTGGATATGGGGTTTGATCCTCAGCTACGGAAGATTGTCTCTCAG ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAG
genomic: GGATGTTGGATATGGGGTTTGATCCTCAGCTACGGAAGATTGTCTCTCAGgttggcttta ... ttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
atctgat putative branch site (score: 4)
tcactttttttttgtt CT-rich tract
actttttttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaatccaattcgatttagaaagacagattgctgaagttgcattttaaaatttctttattctgctggtcatctgatcactttttttttgttttacttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTTGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - -gaaagac
- - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctga