Sequence
atgc intronic sequence ATGC exonic sequence...aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttgattataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
Basic information
species | Glycine max |
transcript | GLYMA09G28530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 11
--aatttgtggctatatattgtta---ttctaattaatttacagaatgcaaacgta-ttgtgtttcaacttgattataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
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gtaacgtcctgctttctaacattaaaatggtggataattcgcatacagaaaccacaattctcacacggttttcttgttacctcga----cgca-------acgcagGTGCTGCAGGATAATTTGGAATGGGAGGATGTGCAGTGGTCGCAGACTGGTGTTTGGGTTGCTGGAAAGGAATATCCTCTCGCCCGAGTGCATTTCCTAT
upper sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttgattataaattcgaattctgcattttctgatg---cagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
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--------gtta-acatttttctccaatttgactcttcttgttttga-aaattctttataaaacaaatgctgatgatgtgttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
upper sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
-aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttga-ttataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
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taccaaatatccaaatggtgatgagctattcacaaaacttaa-atatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttga-acagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTATMapped 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|26268944|gb|CA820007.1|CA820007EST: AGAAACTGATGCGCACGATTGGAATCCCTCTGCCTCTTGAACATGTGGAG GTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGC
genomic: AGAAACTGATGCGCACGATTGGAATCCCTCTGCCTCTTGAACATGTGGAGgtatttttca ... tctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgtattgtgtttcaacttgattataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
ttctgat putative branch site (score: 3)
cattttct CT-rich tract
aacttgattataaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttgattataaattcgaattctgcattttctgatgcagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -gtggcta
- - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt