Sequence
atgc intronic sequence ATGC exonic sequencegttagtaacttatgtcaatatatcagagcttacattaatttcttttatcctttgctttgatatgtatttgaagtatttaatatgtacaaagtgctgatgataatttttattataagcatgacacccttgtaatttatttcttattatgggttgatgtatttgcatgctatcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCTGATCATCTCTCAAATGAAGGAAAAGATTTTGTTAGGAAATGTCTTCAGC
Basic information
species | Glycine max |
transcript | GLYMA20G30100.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 9
gttagtaacttatgtcaatatatcagagcttacattaatttcttttatcctttgctttgatatgtatttgaagtatttaatatgtacaaagtgc-tgatgataatttttattataagcatgacacccttgtaatttatttcttattatgggttgatgtatttgcatgctatcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCTGATCATCTCTCAAATGAAGGAAAAGATTTTGTTAGGAAATGTCTTCAGC
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----------------------------------------------------------------------------ttgaaatgtaaagacttccttcttttgactcgtaatgagacttggaagtttcaccgaagcaact-ttggcatgaac--atttcccctcttttctttcctgcagATTGCTGCAATGTTCAAGATCGGAAATAGCAAGGAACTTCCACCAATACCAGATCACCTTTCAGAGCCAGGCAAGGACTTCATCAGAAAGTGCCTGCAAC
upper sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 8
gttagtaacttatgtcaatatatcagagcttacattaatttcttttatcctttgctttgatatgtatttgaagtatttaatatgtacaaagtgctgatgataatttttattataagcatgacacccttgtaatttatttcttattatgggttgatgtatttgcatgctatcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCTGATCATCTCTCAAATGAAGGAAAAGATTTTGTTAGGAAATGTCTTCAGC
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---------------------------------------------------------------aaatctaaggta--gaattcttaca---ttccaatcgtgcaggttatttgatgttt-----ctttgttcttt-cttctaattatg---tgatgttcacatgttctggtctaa-agGTTGCTGCAATGTTCAAGATTGGGAATAGTAAGGACCTCCCAGCAATTCCTGATCACCTTTCAGATGAAGGTAAGGATTTTGTAAGGCAGTGCTTGCAACMapped 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|18690804|gb|BM519652.1|BM519652EST: CAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGTATGAAGGG GTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCT
genomic: CAGTTTTGGAAATGGCTACAACCAAACCTCCTTGGTTTCAGTATGAAGGGgttagtaact ... atcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttgtaatttatttcttattatgggttgatgtatttgcatgctatcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCTGATCATCTCTCAAATGAAGGAAAAGATTTTGTTAGGAAATGTCTTCAGC
ggttgat putative branch site (score: 5)
taatttatttcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaacttatgtcaatatatcagagcttacattaatttcttttatcctttgctttgatatgtatttgaagtatttaatatgtacaaagtgctgatgataatttttattataagcatgacacccttgtaatttatttcttattatgggttgatgtatttgcatgctatcataacagGTTGCTGCCATGTTCAAGATTGGTAATAGCAAGGAACTCCCAACCATCCCTGATCATCTCTCAAATGAAGGAAAAGATTTTGTTAGGAAATGTCTTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA