Sequence
atgc intronic sequence ATGC exonic sequencegtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttctttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA18G03830.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaaca--aaagctag--agtttgcattc-tacttttcttt-cagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
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------acgaa--aattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 11
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttctttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
| || |||| || || | ||| | | | | | |||| | | | | | | | | || | |||||||| |||||||| || ||||||||||||||||| || || || | || ||||| || ||||| || |||||||| |||||||| |
---------------------gtaagtgtaatata-tcatgaaaataatgattctaccaatatgcatgataagcctaaactcataatatgttctac----agCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGG
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttctttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
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---------------gtgagcgta-atatattatgaaaatgatga--ttgtaccattatgccta----ataagcctaaactcataatacactctac----agCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttct--ttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
||| ||||| | ||||| | | | | | | ||| | ||| || | || || | | ||| ||| | | ||| | ||||| || |||||||| ||||| ||||||||||||||||| ||||| |||| || || | || || ||||| || || || || ||||| |
-------gtaagcagatagatacatatgaatggcaagtccccagaagtg----attagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacattggtacctttaacaaaagctagagtttgcattctacttttctttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
ctttaac putative branch site (score: 3)
tttgcattctactttt putative PPT
tttaacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttctttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA