Sequence
atgc intronic sequence ATGC exonic sequence...agtaataatattagttgagtttttagttcagctgaagttatagtaaattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G25830.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 3
-agtaataatattagttgagtttttagttcagctgaagttatagtaaattttctcttgagaatatt--acctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
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aagtga-ggcactgttccatttcctaaaa-atataacctcattgggggcttctctgtaattttgtttaacatttacttatatttattt-atactatgattcagTGTACTTATTAGACCACATCCTGCCATTTGGCGGCTGGTCCACGGGATGGCAGTTGTTTACCTTGTTGCTCTAACTTTTTTGCTTTTCCAG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 3
agtaataatattagttgagtttttagttcagctgaagtta--tagtaaattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
| | | | |||| | || | | | ||| || ||| | | | | || | ||| | || || || | ||| || | || ||||| ||||||||||| |||||| | | |||||||| ||| | ||||| ||||| || |||||||| || ||||||||||||
--tgaacaaaacagttacttccttgaagtatatagatttagttattaaggtatattgagtttatgcaaactgttactgacaattatttctgctacgatttagTGGACTCATTAGACCACATCCTGCCATTTGGAGGCTTGTTCATGGGATGACAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTTCAG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
agtaataatattagttgagttttt-agttcagctgaagttatagtaaattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
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-ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G15110.1 (Arabidopsis thaliana), 3'ss of exon 4
----agtaataatattagttgagtttttagttcagctgaagtt--atagtaaattttctc-ttgagaatattacctg-aatatatttttttttca-----tgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
| | || | || || || ||| || | || ||| | | || | ||| | ||| || || | | ||| | | | || || ||||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || | ||| ||||||| || || |||||||| ||||||
gtttgtttaccatctcagctgttttattaatttgctttctcttttataatgtagattgtggttgttggtgatacttgtgatgtgtctttaatcaagtaatttgctttatgcagGGTTCTAATCAGGCCCCATCCTGCAATCTGGCGCTTAGTTCATGGAATGGCCGTCATTTACTTAGTTGCACTTACTTTTTTGCTCTTTCAG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 4
agtaataatattagt-tgagtttttagttcagctgaagttatagtaaattttctcttgagaatattacctg-aatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
| | | | || || | |||| | | | | ||| || | || ||| ||| || || | | || || | |||| | |||||| ||||||||||||||||| ||||||||||| | |||||||| ||||| || | ||||| ||| ||||||||||||||||| |||
--tgctgacaccagaatgggattttgatgttgatactactgaagttcataaacatttccagttatgcactgtaaaatttgtagttgtcttttttttttacagGGTACTTATTAGGCCACATCCAGCAATTTGGCGACTAGTTCATGGGATGGCGGTCATTTACCTTGTTTGTCTCACATTTTTGCTTTTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
tttttttttcatgttt CT-rich tract
aatattacctgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaataatattagttgagtttttagttcagctgaagttatagtaaattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - cagctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa