Sequence
atgc intronic sequence ATGC exonic sequence...catttctacgtactagtaatagttgccaccagttttttagtctatatatgtatatgctaatccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
Basic information
species | Glycine max |
transcript | GLYMA13G05060.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 14
-----------------catttctacgtactagtaatagttgccaccagtttttt--agtctatatatgtatatgctaatccag---agttttgaattaactttatc---tttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
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gtaagccaatccagaattagctgtctgtgcaagtttattcttctattggcttgccacaattcgcaaacttgttaatttagtcagtttgatcttctatttactcaaccaaatttatat-tatctagGTCTGGCCGGGAAAGTGACAGTGATGCTGAGGATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAG
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 15
catttctacgtactagtaatagttgcca-ccagttttttagtctatatatgtatatgctaatccagagttttgaattaactttatctttgtat-atatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
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tattgacgaatatgcttcattgacattaactagtgatgtaattcatgagtacaattttaaatctggcaact--aacttattgtatttatgtttgatgtttagATCAGGT---GAAAGTGATAGTGATGCAGAAGACCTTGAACACGCTGACAAGCTTCGGCAAGTTAAAGCCGTTCTTGAAGAG
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
------------------------------------------------------------------------catttctacgtactagtaatagttgccaccagttttttagtctatatatgt-atatgctaatccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
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gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
upper sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 14
catttctacgtactagtaatagttgccaccagttttttagtctatatatgtatatgctaatccagagttttgaattaactttatctttgtatat-atttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
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taactgaaaatggcaaacacacttttaatttgcatattgactcttatgctaggatagca-ttaatgattatgaactaatgacaaaatttcatattatttagACCTGGTCGAGAAAGTGACAGTGAAGCAGAAGATCTTGAGCATGCTGAAAAACTTCGTCAAGTTAAAGCAGTCCTTGAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgtatatgctaatccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
aattaac putative branch site (score: 2)
agttttgaattaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttctacgtactagtaatagttgccaccagttttttagtctatatatgtatatgctaatccagagttttgaattaactttatctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - -tgccacc
- - - - - - - - - - - - - - - - - - - - - - - - - tatatgc