Sequence
atgc intronic sequence ATGC exonic sequence...tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
Basic information
species | Glycine max |
transcript | GLYMA16G26940.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
------------tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggata-attaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
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gtaagttactgcacaatctccctgtgctaaattcaga-gtaaaaatgtaaagcagtcaggt-taagcaagagactgatgcatgaagctgctgctgttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
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-----gtaa-gactcgaaaatcaagactgtatgacctaatcgaatctaaagccactcgatcaaaaca-ctgatttgtg-ttatatctgtgtga-----agAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
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gtatgtatgagtctctcaacaactt---acctttgacagaccaagtactcgaacaaaaccgattttgatcagat--tagttgtttccg-gtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
upper sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
--tcactttagtggttccaaattctt--ttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
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tgatgctagagctgtaatgaatgttgaattttataaaaactgacaatgaatgtgcacacatttgcatggtagtaaaact----cggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
atgtaac putative branch site (score: 3)
attataaggataatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - -tggttcc
- - - - - - - - - - - - - - - - - - - - - - - - tgtaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat