Sequence
atgc intronic sequence ATGC exonic sequence...tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
Basic information
species | Glycine max |
transcript | GLYMA17G30020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagctt--atgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
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taagtaaatttgaagaaatgcgtgatg--cgagatcttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g08610.4 (Oryza sativa), 3'ss of exon 3
tttgatatttta-atgtattgtttcatgattataactttcaagtattggaatatgtaatagctta-tgaagctgctaagcccttgttct-tcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
||| || | | | || || | ||| |||| | || | || | | ||| | | | || ||| || | | | || | | | | | || |||||||||| || | || || || |||||||| ||||| ||||| |||||||||||| | ||||| |||||||| |||
---aataaactacgtatggtcttccagagatttaagtttcccatgttttattaacttttcctttagtccaagttctgagctacagtcttaccatttgttttagGTTCCAAGCTTTTGCTGATCACTTCAAAATGGCTCTGGACTGTTTCTTTGCTGTGTGGTTCGTTGTGGGAAATGTATGGGTATTTGGTGGACATTCTTCT
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
---tttgatattttaatgtattgtttcatgattataactttcaagt---attggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
| || || || | | | | || | | | | | | || || | | |||||| | | | ||| | ||| | || | | || | || | | ||||||| | || | ||||| || |||||||| |||||||||||||| ||||| ||||| || ||||| | | | |||
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttc------tgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATT-CATCT----------------------------------
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------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116952_T07 (Zea mays), 3'ss of exon 2
--tttgatattttaatgtattgtttcat--gattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgt-tcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
|| | | || | || || | || | || | ||| | ||||| || ||| || | || | | || | | | |||| | | || | | ||||||| | | | | || || || ||||||||||||||||||||||| ||||| ||||| ||||| || | |
tcttgaagaattgagtggtctgatatattgagtcattagttttat---ctggaaactgaaatgaacattgtggt--ctgaactctgaagtgattacatattacagGCTTAGTGTGCTGGCTTATCACTTCAAGACAGGTGTTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATT
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G092244_T03 (Zea mays), 3'ss of exon 2
tttgatattttaatgt-attgtttcatgattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
| | || | || | || | ||| |||| ||| | ||| || | || ||| | || | | || | | | | || ||||||| || | | || ||||| || ||||||||||||||||| |||||||| ||| | ||||| |||||||| ||
cctactgttctcatttgatagcagcatacctatacaggtcat-cagaatcataaatactttgttggcaagttttctctgagctgcattctcctcgttgtagGGCCCAAGCTTTTGCTGATCACTTCAAGATGGCGCTGGACTGCTTCTTCGCTGTATGGTTTGTTGTGGGAAATGTGTGGGTGTTTGGTGGACATTCTTCC
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------------------------tttgatatttta-atgtattgtttcatgattataactttcaagtattggaa-tatgtaatagcttatgaagctgctaagcccttgttcttc----ttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
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gtaaacacacatgttcttagatgatctgtttcaactgaaagtttggattttgaattacgttttctctcaaagcttttcttatttttgagaattgagagtttagatgtctcttttgttctaaactttttctttgtgttgaaaatatctgcaatctaattgagtcagtatgattttggtcgttgattttggcttccagACTTAAAGTTATCGTGGAATACTTCAAAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCT
upper sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
tttgatattttaatgtattgtttcatga-ttataactt-tcaagtattgga-atatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
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--taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccc-tggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
cccttgttcttcttgc CT-rich tract
tatgtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgatattttaatgtattgtttcatgattataactttcaagtattggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT
- - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagctgc