Sequence
atgc intronic sequence ATGC exonic sequence...aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctttgtcatccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
Basic information
species | Glycine max |
transcript | GLYMA20G31640.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g32300.1 (Oryza sativa), 3'ss of exon 4
aaagcttatacacaagcacaactgcacaagcc---agttggaacttggaactagttgttttttatcc-tttgtcatccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
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----attactgccatgtcctatgtggtgacctcttaattgaaaattttgatctctgacctgtgatctgtcagatggactgaaacctaccataaatctttgctagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCTGCTATCAAATATCTAC
upper sequence: GLYMA20G31640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g25890.1 (Oryza sativa), 3'ss of exon 1
aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctttgtcatccttactc--attttctgcc--attatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
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-aacgttactgccatgtcctgtatggtggcctcatttaaaaatg---ttgatcttcatctgtgctctgtgggttggactggaatttaccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
upper sequence: GLYMA20G31640.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G22700.3 (Arabidopsis thaliana), 3'ss of exon 3
aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctt-tgtcatccttactcattttctgccattatctca-gGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
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gaacattagactta--tttaagtagctatgcttgctcaacgtttttgttaatttgatcaaatctggatgctatggttctattgttgtctttatgacctgaagGAGCAAGTAAGGAGCGGAGATGCAAGTGCAACAGAGCTCTTTGAGCTTGGTGCAGTGATGTTGAGAAGGAAGTTTTATCCTGCAGCCAACAAGTTTTTGC
upper sequence: GLYMA20G31640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0072g00860.t01 (Vitis vinifera), 3'ss of exon 4
aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctttgtcatccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
|| | | | | | || | | ||| | | | || ||| || ||| | | | | || ||||||||||||||||||||||||||| |||||||||| || ||||||||||| ||||||||| |||| ||||||||||| || |||||||| || |||||||
gttttttctgaaggaaatttatttttcattataatgtatactaaagagtggctggcaggaatctgtttcttatattatgcctctctttttggaatttcagGAGCAAGTAAGAAGTGGTGATGCCAGTGCAACTGAACTGTTTGAACTTGGAGCAGTGATGTTGCGGAGGAAATTTTATCCAGCTGCTACTAAATTCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactagttgttttttatcctttgtcatccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
tccttac putative branch site (score: 2)
ttatctc putative PPT
ttgttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctttgtcatccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - caagcac
- - - - - - - - - - - tgcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgcc