Sequence
atgc intronic sequence ATGC exonic sequence...ctctaatatactattaactctataatggttaaagagaatattttatgtgacatttcctgtattcactttgcctgacttcttggattcatattcttattagTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
Basic information
species | Glycine max |
transcript | GLYMA16G01590.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 2
ctctaatatactattaactctataatggttaaagagaatattttatgtgacatttcctgtattcactttgcctgacttcttggattcatattcttatt---agTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
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ttttatcaagttattggcctttgaa--atttcacactttattacttttt-cgtatcttattagtgctccatgtaagagcttcattttggttctttatttccagTTTTGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCATCGGCGCATGGCGTCACGGAAAGAAAAGCCACGCATCCTGATCCTTGGTGGTGCACTT
upper sequence: GLYMA16G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G153722_T01 (Zea mays), 3'ss of exon 2
-ctctaatatactattaactctataatg-gttaaagagaatattttatgtgacatttcctgtattcactttgcctgacttcttggat-tcatattcttattagTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
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gatctattacgttttgagtttcatactgtatttatctgtgcatttctttgg---tttccaccagttcttttttttggttttatacatcttcctttatttgcagTTTCGTTGTAAAAGGAGTTGTTTGTAAGAAGAATGTTGCTCACCGGCGTATGTCATCAAAAAAGGAAAAGCCTCCAATCTTGATTCTTGGTGGTGCACTC
upper sequence: GLYMA16G01590.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g00380.t01 (Vitis vinifera), 3'ss of exon 2
----------ctctaat--atactattaactctataatggttaaagagaatattttatgtgacatttc--ctgtattcactttgcctgacttcttggattcatattcttattagTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
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gtaaatgttttgataatttatgttatctttcatatagcatccatcatgatgctcttgttgcatatctcaacttctttcccttcga-tgaagattttgattacttttcttgc-agTATGGTCATCAAAGGAGTTGTTTGTAAGAAAAATATAGCTCATCGAAGAATGACATCAAAAATAGAGAAACCACGCTTGTTGATCCTTGGAGGAGCTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgacatttcctgtattcactttgcctgacttcttggattcatattcttattagTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
gcctgac putative branch site (score: 3)
ttcttatt putative PPT
attcatattcttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctaatatactattaactctataatggttaaagagaatattttatgtgacatttcctgtattcactttgcctgacttcttggattcatattcttattagTGTGGTGGTTAAAGGAGTTGTTTGTAAGAAAAATGTGGCTCACCGGCGAATGACGTCAAAAGTGGATAAACCTCGCTTGTTGATCCTTGGAGGGGCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - aaagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg