Sequence
atgc intronic sequence ATGC exonic sequence...cccaaattttaaggacaagaaatatatttaagcgttaatatccagtaaattggcatttgcaggattttattgtcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
Basic information
species | Glycine max |
transcript | GLYMA18G47310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47310.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g12560.1 (Oryza sativa), 3'ss of exon 2
-cccaaattttaaggacaagaaatatatttaagcgttaat---atccagtaaattggcatttgcaggattttattgtcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
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gtgtggttctcttgattttgttggttacttggctcttagcctgattcatgttctttcttcatgtatagatttgcc-ccatgctgttctgctt--gtttgtgtagGTTGTGGAGACAGCACTTGCCTTGCAGGAGGCTGGCTGCTTCTCGGTTGTGTTGGAGTGTGTGCCAGCTCCTGTGGCAGCTGCTGCAACATCAGCATTGC
upper sequence: GLYMA18G47310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010596_T02 (Zea mays), 3'ss of exon 2
---------------cccaa-attttaaggacaagaaatatatttaagcgttaatatccagtaaattggcatttgcaggattttattgtcatccta-ataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
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gtttgccgctagctgctcattatgtttgtggcttggt-tatatttgttgctacacatttggtgctggtgcgctgactgactggtagggtctcactccatgctattgtgcttgtgtagGTTGTGGAGACAGCACTTGCCTTGCAGGAGGCTGGATGCTTCTCGGTTGTGTTGGAGTGTGTGCCTGCTCCAGTGGCAGCAGCTGCAACATCAGCATTGA
upper sequence: GLYMA18G47310.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G61530.2 (Arabidopsis thaliana), 3'ss of exon 3
-cccaaattttaaggacaagaaatat--atttaagcgttaa-----tatccagtaaattggcatttgcaggattttattgtcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
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gtttgaatgtaatggttcaggcatgtgtatgtaatccttaagaggttattttttaaaggggtgtgtg-ataaaattatttttctcttatttgg--tggatt-----agGTTGTGGAAACTGCTATGGCTTTGCAAGAAGCTGGATGTTTTTCGGTTGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTA
upper sequence: GLYMA18G47310.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02170.t01 (Vitis vinifera), 3'ss of exon 2
----------cccaaattttaaggacaagaaatatat--ttaagcgttaatatccagtaaattggcatttgcaggattttattg---tcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
| | || || | || || || | ||||| || | || | | | | | ||| | | | | | | | |||||||||||| ||| ||||||| |||||||||||||| ||| |||||||| | || |||||||||||||||||||||||||| | ||| |||| ||||
gtccttctctttccatttgtattcttgggggatttaggattcaaaaaaaatatatcgttaggtgctgtcaagatctctctctaaaatccatgttgaattggtttgatttgagcagGTTGTGGAGACTGCAATGGCTTTACAGGAAGCTGGGTGTTTTGCTGTTGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaattggcatttgcaggattttattgtcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
tcctaat putative branch site (score: 2)
taataagaataagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccaaattttaaggacaagaaatatatttaagcgttaatatccagtaaattggcatttgcaggattttattgtcatcctaataagaataagtctatgaagGTTGTGGAGATGGCATTGGCTTTGCAGGAAGCTGGGTGCTTTTCTGTTGTTGTAGAGTGTGTGCCTGCACCTGTGGCTGCTGCTGCTACAGCAGCACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
cccaaat
- - - - - - - - aagaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaataa