Sequence
atgc intronic sequence ATGC exonic sequencegtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
Basic information
species | Glycine max |
transcript | GLYMA14G12220.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g56450.1 (Oryza sativa), 3'ss of exon 1
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
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----------------------aatcaacgttgtcatggtagcttgattttatggtgtaaatgcagttattaggactgttgc-tctcctatttgctcaacatttctcattctttttttgc-cagCCAGAATGGTAAGTTTAGCTATGGGTATGCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAG
upper sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
| | | || || || | || | | || | | ||| ||| | || | |||| ||| | || || || || | | |||| ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||| || || ||||| || | |||||||||||| ||||| ||
---------------gggagtgttagttt-cgaatatctgtatatagccattgacagagaattcg---tttctgttatt---attacctgatattgttgttcttcttgtg--ttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
upper sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 1
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
||| | ||| | | | || | | | | | | | | | | || || || || || | || ||| |||| |||| ||| | | || |||||||| | ||| |||||||| ||||| ||||||||||| || || | || |||||||| || |||||||||||||||||| ||||||||||| |
-------ttgt-tacagtagcttggctccaaatatcaaatcagtggactatcatgt-tgttcttgtattacctatttgttcagtg-------tttcacat-----ttattttttctgcc---agCCAGAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAG
upper sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA----
| ||| | | | || | | | | | | | | | | || || || || || | || ||| |||| |||| ||| | | || |||||||| | ||| |||||||| ||||| ||||||||||| || || | || |||||||| || |||||||||||||||||| ||||||||||| |
------------tacagtagcttggctccaaatatcaaatcagtggactatcatgt-tgttcttgtattacctatttgttcagtg-------tttcacat-----ttattttttctgcc---agccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG
upper sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 2
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatt-tctgggtttttagttgattgaatgatatgattttgacat-gtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
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--------------------ttgaggaccttataatgtttggttttatctttcta-atatcatctacaacaataa--gagtgcacaggatcttcctaacatagtgtgagatgttgtctaac---agTCATAATGGGAAGTTCAGCTACGGATATGCTAGTTCTCCCGGGAAAAGGTCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
ttgtaac putative branch site (score: 2)
aatgatatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA