Sequence
atgc intronic sequence ATGC exonic sequence...attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
Basic information
species | Glycine max |
transcript | GLYMA16G23880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23880.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 2
attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgtt-ttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
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---------------------gtgagtactacggccacactgtatccttggtgattttgttttagatcatgcatctcttaggca---atgtgaacttgcagTATCTGAGCAATGGGAGGTTCAAGAACGCGGATCACCAGGCGGTGGTGAACTCCGACTGCTGCCGGCTGTCGATCGCGACGTTCCAGAACCCGGCGCCGG
upper sequence: GLYMA16G23880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51240.1 (Arabidopsis thaliana), 3'ss of exon 2
attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
| || | | || | ||||||| || | || |||||| | | | || |||| | ||| | || | ||| ||| | |||||||||| |||||||||| |||||||||||| || ||||||||||| ||| ||| | || |||||||||||||| || ||||| | ||
--------gttagtactctatccatttattggctttt--ttgt-ttctctgtttttggttttgacttggtcaa-tcttgatt-----tgtcttgatgaagTTTTTGAGCAATGGGAGGTTCAAGAATGCTGATCATCAGGCCGTGGTGAACTCTAACTCGAGCAGATTATCCATAGCCACGTTCCAGAACCCCGCGCCGG
upper sequence: GLYMA16G23880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g14310.t01 (Vitis vinifera), 3'ss of exon 2
---attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
| || | | | | || | | || | | || | | ||||| | ||| | | || | | || | |||||||||||||||||| |||||||| | ||| || || ||||| ||||||||||| || || || ||||| || |||||||| || ||||| | |||
gtgagtagtgattctctgcttattcctcttttggattccccatcgaaggggcagaataatataattaatta-----actctgcattcgattg-acgtgggcagTATCTGAGCAATGGGAGGTTCAAAAATGCGGACCACCAAGCTGTGGTGAACTCCGACTGCAGTCGGTTGTCGATTGCCACGTTCCAGAACCCAGCCCCAG
upper sequence: GLYMA16G23880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 2
------attaat-tttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
| || | | || | | || | | || || | | || || || | | | ||| | ||| ||| | ||||||||||||||||||| |||||||||| ||||||||| ||||||||||||||||| || |||||| | |||||||||| || || |||||||| | |||
tatgtggtcaacatccacaatagtcct-tcctgatatggtattcaaattcatgctacccgaacccgaaagagagagt--gattattggtttgg-tatg---gtgcagTATCTGAGCAATGGGAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCCAATCATAGCAGACTGTCCATAGCAACATTCCAAAACCCCGCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
ttttccataataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaattttattttatttttatcaagcaagggcttttgaccgtgtactttgttttccataataatttattcaaattttgggtgtgggtgcatccatgcagTATCTGAGCAATGGAAGGTTCAAGAGTGCTGATCATCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACGTTTCAAAACCCTGTACCAA
- - - - - - - - - - -tcaagca
- - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtg