Sequence
atgc intronic sequence ATGC exonic sequence...gctgaaatttcaattaaatgacaatgaatttaaacacttatataaatatattgtaaaaggctttaattttttcttgttttcaaaatgttcttaactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAAATACCAAGTGCTCATCGCATTATCATTAGCGGCACTCCTTTGCAAAATA
Basic information
species | Glycine max |
transcript | GLYMA08G00400.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G63950.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------gctgaaatttcaattaaatgacaatgaat-ttaaacacttatataaatatattgtaaaaggctttaattttttcttgtttt--------caaaatgttctt--------aactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAAATACCAAGTGCTCATCGCATTATCATTAGCGGCACTCCTTTGCAAAATA
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gtaaacacatcaatattttatcatttgtgaggtctttgcactaatagttggtatagtgtgtatgcactattgtccatcaagcgctgagatgttaccattagtgtaggttctgaattttccccctactgatatcaataaaatgtatttccgcttacacttctagGGACATCTTATTAAGAACCCCAACACACAAAGGGCGAAGAGTTTGCTTGAGATCCCAAGTTCTCACCGTATTATAATAAGTGGTACACCAATCCAGAACA
upper sequence: GLYMA08G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0044g01680.t01 (Vitis vinifera), 3'ss of exon 5
-gctgaaatttca-attaaatgacaatgaatttaaacacttatataaatatattgtaaaaggctttaattttttcttgttttcaaaatgttcttaactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAAATACCAAGTGCTCATCGCATTATCATTAGCGGCACTCCTTTGCAAAATA
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cattttcattttatacaaaatcttgctttacttgtacataagggaaactttattttgtaaatatttactttttaatccattt--atctatttttatttgtagGGACATCTCATAAAGAATCCCAGTACACAAAGGGCTAAAAGTTTGATGGAAATACCTTGTGCTCATCGTATTGTTGTTAGTGGCACACCAATACAAAACAMapped 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|151402061|gb|EV271874.1|EV271874EST: ATGAGGATAATGAAGAAGGCGCAACATGGGACTACATGATACTTGATGAG GGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAA
genomic: ATGAGGATAATGAAGAAGGCGCAACATGGGACTACATGATACTTGATGAGgtaaggatcg ... ttaactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatattgtaaaaggctttaattttttcttgttttcaaaatgttcttaactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAAATACCAAGTGCTCATCGCATTATCATTAGCGGCACTCCTTTGCAAAATA
tcttaac putative branch site (score: 2)
tgttctt CT-rich tract
tttaattttttcttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctgaaatttcaattaaatgacaatgaatttaaacacttatataaatatattgtaaaaggctttaattttttcttgttttcaaaatgttcttaactttagGGACACCTTATAAAGAACCCAAGCACACAAAGGGCTAAAAGTTTGCTTGAAATACCAAGTGCTCATCGCATTATCATTAGCGGCACTCCTTTGCAAAATA
- - - - - - - - - - -caatgaa