Sequence
atgc intronic sequence ATGC exonic sequence...tttgttattatctcttaaatgcctttcatttcttattgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
Basic information
species | Glycine max |
transcript | GLYMA09G39770.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 8
--tttgttattatctcttaaatgcctttcatttcttattgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
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tgccatttacaggaaaaaaaatgcattgacctgactagtgttaatgtaatctaagtctttc-ttctgatagatatttgttgtgacatactgtt-gtatgcagGATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTTATATCACCTAATTCTTCAAAAGGAGGG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 7
----tttgttattatctcttaaatgcctttc-atttcttattgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
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cttgcatggcatactcattctgaagcattgcgagccttcaatcctttagtaatgttaatct---agcttgccttt--ttaatatattttctcgtgttgtccccagGATTTGGCTGTGGTGGTCCTGTTGATATTAATACCTCTCATATCACCTAATTCTTCAAAAGGAGGG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 7
tttgttattatctcttaaatgcctttcatttcttattgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
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---------gtttgttcag-aacacaaagttgttactgcgcttgtataaaggctatc--atgctgg-gtaactc--ttttcaatctgttggtcttcacagGATCTGGCTGTGGTCGTGTTACTGATTCTCATCCCACTTATTTCACCTAATTCATCCAAAGGAGGG
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 6
tttgttattatctctt-aaatgcctttcatttctta---ttgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
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--tttaattatttagtgaaattttgtttatgttgaaatcttgaacatgatttgaaagtttcctttttcttttcatcttggttttt--ttgttctcttttttcagGATTTGGCTGTTGTGGTTCTTCTAATACTCATACCTCTGATTTCACCAAATTCATCTAAAGGAGGGMapped 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|16996864|gb|BM086236.1|BM086236EST: CATGGCCGAGCTACTTTTTCTGTGTTACTTTTTCAG GATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAAT
genomic: CATGGCCGAGCTACTTTTTCTGTGTTACTTTTTCAGgtgcgttatc ... ttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
aattgac putative branch site (score: 3)
cttttactctttgttt CT-rich tract
aactttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgttattatctcttaaatgcctttcatttcttattgtattggttttgcaactttttgattttgacacaaattgacttttactctttgtttatattcagGATCTGGCTGTCGTGGTCTTGCTAATACTCATACCTCTTATTTCTCCTAATTCTTCCAAAGGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - -aatgcct
- - - - - - - - - - - - - - - - - - - - - - - -tgcaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaca