Sequence
atgc intronic sequence ATGC exonic sequence...tctcgataccttctcatagcgagggccaagggtgaggagccttctggcagcagagtaagttagttttttgttgatttcttttgtactgttttgcttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGCATTAAGTGAAAAATCACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
Basic information
species | Glycine max |
transcript | GLYMA17G09080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 3
tctcgataccttctcatagcgagggccaagggtgaggagccttctggcagcagagtaagttagttttttgttgatttcttttgtactgttttg-cttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGCATTAAGTGAAAAATCACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
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--gtagtttgtcctta-aataataattcccagtttgtcactttttagtattgtaaatatatggtcatatgtctttatgttatcttttcttatggcaaacagAACAGTTGATGTCCCTAGCTCTAGGATTGTTATCATTGAAGGCATCTATGCATTGAGTGAAAAGTTACGATCTGTATTGGACCTACGTGTTTCTGTCACT
upper sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------tctcgataccttctcatagcgagggccaagggtga-------ggagccttctggcagcagagta-agttagttttttgt--tgatttctt--ttgtactgttttgcttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGCATTAAGTGAAAAATCACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
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gtatatatattcttcgttggtgcatttactactatttcaa-acttgtggacagacggcgttatacttgaattcctgggaaccacttgttagttgataagagctacacagctgcaatgacttatcagtttcttcgtgctttgtatagAACGCTTGAGGTGCCTAGCTCTCGCATTGTTATTCTAGAAGGCATATATGCTTTGAGTGAGAAGCTACGGCCTTTGCTAGATCTTCGTGTCTCTGTCACTMapped 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|11274567|gb|BF324909.1|BF324909EST: GTTCAAGTTCCAATATACGATTTCAAGTCTAGTTCTCGCATAGGTTACAG GACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGC
genomic: GTTCAAGTTCCAATATACGATTTCAAGTCTAGTTCTCGCATAGGTTACAGgttgtgtacc ... ttgcttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcagcagagtaagttagttttttgttgatttcttttgtactgttttgcttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGCATTAAGTGAAAAATCACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
tgttgat putative branch site (score: 4)
ttttgctt putative PPT
taagttagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcgataccttctcatagcgagggccaagggtgaggagccttctggcagcagagtaagttagttttttgttgatttcttttgtactgttttgcttacagGACTGTTGAAGTCCCTAGCTCTCGTATTGTAATCATAGAAGGCATCTATGCATTAAGTGAAAAATCACGACCTTTGCTTGATCTTCGTGTTTCTGTCACT
- - - - ccttctc
- - - - - - - - - gcgaggg
- - - - - - - - - - - - - - -gggtgag
- - - - - - - - - - - - - - - - - - - gccttct