Sequence
atgc intronic sequence ATGC exonic sequencegtatgctattgcttcctctactttcacttttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
Basic information
species | Glycine max |
transcript | GLYMA20G39090.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G13030.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgctattgcttcctctactttcacttttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
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------------------------taatctactgaactaagcctctagtagagaaatttttgtctataaaattaggcttctaggtggttgactactcctattgtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG
upper sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
gtatgctattgcttcctctactttcactt--ttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
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-------------------atatccagtaggtttttaatgggatgggatatccaggaattgggggat----agtcatagattaaaataattgttta-acttc--gtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAGMapped 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|10709358|gb|BF009082.1|BF009082EST: CTTTCTCTTGTTACCACCGGCAACCTCGTCACCCGTGACATGTTTTATGA CGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATC
genomic: CTTTCTCTTGTTACCACCGGCAACCTCGTCACCCGTGACATGTTTTATGAgtatgctatt ... acacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
ttttaat putative branch site (score: 3)
tgtttttaatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctattgcttcctctactttcacttttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT