Sequence
atgc intronic sequence ATGC exonic sequence...gcactgagtttcttcatttcttttgtttcataccaggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
Basic information
species | Glycine max |
transcript | GLYMA20G33140.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G10540.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------gcactgagtttcttcatttc----ttttgtttca--tac-caggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
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gtaagagttttgtgttagaacaaactttgaccactatgtgatgaatatatggagttttttttttttgaagtagtcttttagttatgtggattactacatatcctcttacttagaacaatttttctttggtatttctggaacttattcaaacagAAATGATCTCTGGGCACTCGGCTGCACTCTGTACCAAATGCTTTCAGGAACTTCCCCATTCAAGGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 6
gcactgagtttcttcatttcttttgttt-cataccaggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
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--gtaagagttttctgtttctgtaatttgcgttttggttttgtggattgcgatgcctctcttactttgtacaatttc-tttggtactctgtggaacaccagGAATGATCTTTGGGCTCTCGGCTGCACTCTCTATCAGATGCTTTCGGGGACTTCCCCATTTAAAGATGCAAGTGAATGGCTGATTTTCCAAAGAATTATA
upper sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 7
gcactgagtttcttcatttcttttgtttcataccaggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcaca-acagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
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gaaaaaaaaagaagaaaagtgttggtttca-atggttctgtcagatcatgtactttctttggtggataacatatttactgttgttaacttcatacatacagAAACGATCTTTGGGCACTTGGCTGCACTTTGTACCAGATGCTTTCTGGAACTTCTCCTTTTAAAGATGCAAGTGAATGGCTTATTTTCCAAAGAATTATAMapped 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|208074095|gb|GD872030.1|GD872030EST: GCTGCTTATGTTCCTCCAGAGGTTCTTAATTCCTCTCCAGCAACTTTTGG AAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAAC
genomic: GCTGCTTATGTTCCTCCAGAGGTTCTTAATTCCTCTCCAGCAACTTTTGGgtagggacta ... atcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
taataac putative branch site (score: 1)
tgttttttgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcactgagtttcttcatttcttttgtttcataccaggtccctatataataacttttcttctgttttttgtttttttgccctcaaatatatatcacaacagAAATGACCTTTGGGCACTTGGCTGCACATTATACCAAATGCTTTCTGGAACTTCCCCTTTTAAAGACGCGAGTGAATGGCTTATTTTTCAAAGAATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- -ctgagtt
- - - - - -cttcatt
- - - - - - - - - - - - - - catacca