Sequence
atgc intronic sequence ATGC exonic sequence...tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctctcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA03G04500.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 4
--------tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctctcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
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gaaaaagttagaactgcatttctttcatataaaactacaatcttgtatcaaccc-atcataagtgttgtagtg----ctgaaacaagtggcccgtaatttt---ctagGTATGTACTGGAGCGAAGAGTGAACAGCAATCCAAGCTTGCAGCAAGGAAG
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G161418_T06 (Zea mays), 3'ss of exon 3
--------tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctctcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG-------------------------------------------------
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gaaaaagttagaactgcatttctttcatataaaactacaatcttgtatcaaccc-atcataagtgttgtagtg----ctgaaacaagtggcccgtaatttt---ctagGTATGTACTGGAGCGAAGAGTGAACAGCAATCCAAGCTTGCAGCAAGGAAGGTGTGATATGGCTTGATATCATTTTATTTAAGTTGGATCTAGTTTACGG
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 4
tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctc--tcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
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--tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaataatggatagttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAGMapped 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|31461676|gb|CD403704.1|CD403704EST: GGATAAGAGATCCCNAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG GTTTGTACTGGAGCTAAGAGTGAACAACCATCTAAATTGGCAGCAAGGAAG
genomic: GGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATGgtatgatcct ... tattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
EST:
gi|254322493|gb|GR837907.1|GR837907EST: GGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG GTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
genomic: GGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATGgtatgatcct ... tattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtaatggtttctctcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
atttaat putative branch site (score: 4)
aactttaaatttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctctcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA