Sequence
atgc intronic sequence ATGC exonic sequence...ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
Basic information
species | Glycine max |
transcript | GLYMA20G31800.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g01270.1 (Oryza sativa), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctgga-atgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
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-aatattatttctgataatgttactttattgttctattggaaatggatagaggtgattcttgcatgttgttatcctaagctcttttttcttgcttctgcagGAAAGCGATTCTTTGAGGAGTTGGATAGAGATGGTGATGGCCAAGTCACCCTGGAAGACCTTGAAGTTGCAATGAGAAAGAGGCGATTGCCAAGGAGGTA
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g01240.1 (Oryza sativa), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctggaatgacaaatttcactgtcactttcatta-tcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
| | ||| | | |||| | | | || | | |||| | || | | || | || ||| || | | |||| | | | |||||||||||||| || |||||||| ||||| ||||| || |||||||| || || ||||||||||||| || ||||| | || ||
-aatattatgtctgatgatgttactttgttgttctattggaaatagatggaggtaactcttgcatgttgatatcctaagctcttttttgttgcttctgcagGAAAGCGATTCTTTGAGGAGTTAGACAGAGATGGTGATGGTCAAGTCACCCTGGAAGACCTTGAGATTGCAATGAGAAAGAGGCGATTGCCAAGGAGGTA
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G003033_T01 (Zea mays), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctggaatgacaaatttcact-gtcactttcattatcatac---agGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
|| | | ||| | |||| | | || | || ||| || |||| | |||| | | | | || ||| || | | | ||| | | | |||||||| |||||||| |||||||| ||||||||||| ||||| |||||||| ||| |||||| ||| || || | | ||| | || ||
ctgcataacataatgcaatgatacttttgaaaaggtt---gctatttttatg-tattagttggatcataaggtgatatttgtaactgatgttctgctgctgtagGAAAGCGATTCTTTGAAGAGTTGGACAGAGATGGTGATGGCCAAGTCACTCTAGAAGATCTCGAAATTGCAACGAGGAAGAGGCGGTTACCAAGGAGGTA
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G146378_T01 (Zea mays), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggta-tttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
| || | | | | | | | | | || | | ||| || || | | | | | || | | | | | |||| | | | |||||||| ||||| || |||||||| ||||||||||| ||||| |||||||| ||| |||||| ||| || || | ||||| | || ||
-tctgcttaacataatgcaatgatacttttgaaaaggttgctcttttatgtattagttagatcataaggtgatatttgtaactgatgttctgctgctgcagGAAAGCGATTCTTTGAAGAGTTAGACAGAGATGGTGATGGCCAAGTCACTCTAGAAGATCTCGAAATTGCAACGAGGAAGAGGCGGTTGCCAAGGAGGTA
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatc----tttgtggtatttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
|||| |||| | || || | ||| || | | ||| |||| | | | || | | ||| | | | | |||| |||||||||||||| || || ||||||||||| |||||| |||||||| |||| ||||| ||| |||||||||| | |||||| |||| |||||||
---gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactatt-atttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
upper sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 1
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctggaatgacaaatttcactgtcactttcattat-catacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
| ||| | | || ||| || || | || ||| | | ||| | ||| || || | | | ||| | | | | || | || ||| ||| |||||||||| ||| ||||||||||||| ||||| |||||||| |||||||||| ||||| |||||||||| ||||| |||||||| |||||
gtttactctttttgggctggtta-tgctccatcactttttcttttgtttcttcaattatttgcaaggtttattctcattttgaaatcatgcattcttatagGAAGGCGGTTCTTTGAAGAGCTGGATAGAGATGGTGATGGTCAAGTAACATTGGAAGATCTTGAAGTCGCAATGAGAAGCAGAAAACTGCCACGGAGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgtggtatttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
ctttcatt CT-rich tract
tttcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaactatatagggactgactactgtacttacattttaagtcatctttgtggtatttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - -actactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcac