Sequence
atgc intronic sequence ATGC exonic sequencegcaattataattgattttatttcatgtcacgcttttctgttttggattgttcttacttatatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
Basic information
species | Glycine max |
transcript | GLYMA04G43650.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 2
---------gcaatta--taattgattttatttcatg--tcacgcttttctgttttggattgttcttacttatatattggtttg---------tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
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gcagttctcacaattatttagtttaagtcaaacaatgtttcccgatcttcctatctgcatattgctcatgtcattattaatgtggttatggtctctgaagCTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
upper sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 2
-------gcaattataat----tgattttatttcatgtcacgcttttctgttttggattgtt--cttacttatata-ttggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
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gagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagctcacagGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
upper sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G087692_T02 (Zea mays), 3'ss of exon 2
--------------gcaattataat----tgattttatttcatgtcacgcttttctgttttggattgtt--cttacttatata-ttggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
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catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
upper sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 3'ss of exon 4
--------------gcaattataattgattttatttcatgtca----cgcttttctgttttggattgttcttactta---tatattggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
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tgctcttcaatgccttcatcagtatgtatgtagattcatgtaaaaaatatgttgatgtttttattggcactctaatggcttgtatttgtaaattgcaaagTTCTCTAGATCTGGTAATCAGCTGCTTGGGACTCCATTGGACGAATGATCTTCCTGGAGCCATGATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtcacgcttttctgttttggattgttcttacttatatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
ttcttac putative branch site (score: 2)
tttgttt putative PPT
ttcttacttatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaattataattgattttatttcatgtcacgcttttctgttttggattgttcttacttatatattggtttgtttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA