Sequence
atgc intronic sequence ATGC exonic sequencegtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctatta-cctggatacac-aatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
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-----------------------------------gtatataatattgaaatag-tggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttct-cagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 12
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
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---------------------------------------------------------gtaactactcttttgagggggg---ggggggtcttaaccacactgtactattttttattcatgtcattcttactttctaagGCTGAATC-CTCTTCT--CTTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTG----------------
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG-----------
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-----------------------------------------gtaattaatctttgt-gtgtgtgtgtggggggggggggtcttaaccgcactatactattgt-------ttattcatgtcattcctgctttc-taatattgaatcctcttttcttacctc------agTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 12
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
| | || | | | ||| | ||| ||| || | || ||| ||| || || | | | | | | | || | | | || | ||| | | | || | | || | ||||||| |||||||| |||||| | ||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || ||||| |||||
--------------------------gtaagtctttgaccttactttatattaa----tatttcttgatttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaa--gttgtgtag-tgtttaa-gcttacatggaagctaaaaatatatt-gcagTATCTTAGCACAGCAGAGTTTTCCATGCGGGAAGAATTATCACTTAAAGCTGCTATCCTTGCTGAGAAGTTTGCTCCTGATCTATCATG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
|||| | | | | || | | || | | |||| || | | | | | || | | ||| || | | || ||| ||||||| |||||||| || ||| | ||||| |||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||
--------------------------------------------------gtaagtctttgaccttccctcatga----tttgtgaagt--ttaacagaaaggaaggattaagttgg-tagtgtttaagcttacatgga----------acccaaaaatacattgcagTATCTTAGCACAGCAGAATTTTCTATGCGGGAGGAATTATCACTTAAAGCTGCTATTCTTGCTGAGAAGTTTGCTCCTGATCTTTCATG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 11
--gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatg-attagtttgctattccaactgt-ttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
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gtacacaaatattggaagaaaatagta-acttggtttaaaattctcgatcaaatcttctatattcaattttttaa-------tgttgcaccaagaaagtgcagtag--aaatttttcatctggtgcaaaacaaaacaagggatcataccactaacatatgtctgtttttcagTATCTCAGCAGTGCTGACTTTGCTATGCGCGAGGAATTGTCACTAAAAGCAGCAATCCTAGCTGAGAAATTTGCCCCTGACCTATCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
ctgttttt CT-rich tract
aatgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctggatacacaatgattagtttgctattccaactgtttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGATCTTTCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT