Sequence
atgc intronic sequence ATGC exonic sequence...gtcgagattgtactgaacatggttgatacttcatttattggctttcatttcttcttgccaccaagccttattattgtatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
Basic information
species | Glycine max |
transcript | GLYMA20G33300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g39690.1 (Oryza sativa), 3'ss of exon 3
gtcgagattgtactgaacatggttgatacttcatttattggctttcatttcttcttgccaccaagccttattattgtatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
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------gttttttt--atttctttcatgaagaaagtctctgcaa-catatttctttagttctcagcgtaaatactgaattagtgttcattc----tgcagAAGGAGTGTTTCTAATCTTCTTCATAGTGCTTTTCGTGAAAATTTGGACCGACTTATCCGGTCATATGTTGAAAGGCAAGGTCGTGCTCCTCTCTCTTGG
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g01720.1 (Oryza sativa), 3'ss of exon 3
gtcgagattgtactgaacatggttgatacttcatttattggctttcatttcttcttgc-caccaagccttattattgtatgg--atttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTC-GTGCACCAATTGACTGG
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---------gtactt--cttcttttttccaagaaacaagaacatgaaatggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT-
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 4
--gtcgagattgtactga--acatggttgatacttcatttattggctttcatttcttcttgccaccaagccttattattgtatggattttta------ttcatgttt-cagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
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gtactaaaaaggttttagccacatttttgacaaag-gtggatttgttttcgttctttattacc-ttgatttctgtgagattgatgatttctaccgtcttttctgtttgcagGAGAAGTGTTTCTAATCTACTACATAGTGGTTTCCGTGAAAGTCTTGATCAACTGATACAGTCATATGCTGAAAGGAGAGGACACACTCACGTAGACTGG
upper sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 3
gtcgagattgtact-gaacatggttgatacttcatttattggctttcattt-cttcttgccaccaagccttattattgtatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
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---------gtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactcaatagtgggtttttttttgg----cagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCGCCCATTGATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttcttcttgccaccaagccttattattgtatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
tttttattc CT-rich tract
ttattattgtatggat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgagattgtactgaacatggttgatacttcatttattggctttcatttcttcttgccaccaagccttattattgtatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTCGTGCACCAATTGACTGG
- - - - - -actgaac
- - - - - - - - - - - - - - cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgg