Sequence
atgc intronic sequence ATGC exonic sequencegtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
Basic information
species | Glycine max |
transcript | GLYMA17G14240.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g41460.4 (Oryza sativa), 3'ss of exon 1
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| || ||| | | || || ||| | | ||| | | | ||| | ||| | ||| || || | || ||| | | | || |||| || ||||| || ||||| | ||||| ||||| || || ||||| |||||||| || || ||||||||||||||||||||||| |||||||
------------------ttgttgaatccggctacctcctaccttacatacactatacttacaagtcaattgagtcacaattta--attcga---ttagattcctctttttcct-tctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g41460.2 (Oryza sativa), 3'ss of exon 1
---------gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| | | | || ||| | | || || ||| | | ||| | | | ||| | ||| | ||| || || | || ||| | | | || |||| || ||||| || ||||| | ||||| ||||| || || ||||| |||||||| || || ||||||||||||||||||||||| |||||||
gcccgtgccctgccctgcccttccctcttgttgaatccggctacctcctaccttacatacactatacttacaagtcaattgagtcacaattta--attcga---ttagattcctctttttcct-tctctttagGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
|| | | | | || ||| | | || | ||| | ||| | | ||| | ||| | | || || | || ||| || ||| |||| || ||||| || ||||| || || || || || | || ||||| |||||||| || || ||||||||||||||||||||||| |||||||
gtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaattta--acccga---ttagattcctcttttcctt-cttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 1
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| | | | || || | | || || || ||| | | | | | || || || ||||| |||| | |||| ||||| || || || ||||| |||||||| || || || || || || |||||||| || |||||||||||||| |||||||| || |||||||
-----------------------gcacgcacgcacgcacgcgtcgttgaatgataga-gtcccgccg-catgcgtttcgct-cgctggcgttttcatgcgtggtg-tttgtgttgtgt--gtagGCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 2
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| | | | | ||||| | | | ||| ||| || | | | | |||| | | ||||| ||||| ||||| ||||| |||||||| || || || || || || |||||||| || ||||||||||| || |||||||| ||||||||||
---------------------------gtaccctacaacaaggacatg---attttcagcttctttgatatgatttcg--cttcacgtctcatcattgatcgccccccccctccaatggaccagGCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: AC203966.5_FGT002 (Zea mays), 3'ss of exon 2
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCAT-GCTAA
| | | | || | | |||||| || | | | | | | | | | | ||||| ||||| ||||| ||||| |||||||| || || || ||||| || |||||||| || ||||||||||| || |||||||| ||||| |||||
-----------------------------------gtacgctacaacaaggacagtattttcagcttctttgaatt-gatttcgcttcacgtctcatcactgatcgtcccctccaacggaccagGCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTTGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATTGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
|||| | | ||||||| |||| || | || ||| | || | | | || | | || ||||| || | |||| | ||||||||||| || || || |||||||| |||||||| |||||||| || || ||||| | ||||||||||||||||| ||||| |||||||
---------------------gtaaacgctacaataaaccattttttttatagttgccaaaacat-gatatatatctaatctt----caagagcctgagaattgcttttgtcttttgattacagTCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgt-tattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| | | ||| | | | | | || | || ||| | | | || | || ||| |||| ||| |||| || ||| | || ||||| || || || || || ||||| |||||||| |||||||| || || ||||| | ||||||||||||||||| |||||||||||||
-----------------------------------gtaacacatcaaataaagtgtttttatcattagtatgggtttatctctatataatcgaggatt--gtttctgtttctttt-cttttgcagTCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA
upper sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 2
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
| ||| |||||||| || |||||| | | | | |||| | | | | | | || || ||| |||||| ||| |||| || |||| || | || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||||||||||||||| |||||||
----------ctttagag----caaatttgcagctccactattttgtgtggggtgtgtttgtgtttattctcatt----acattttgttgtaatatt--ctttccattt-ttctgtt---gtagTCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
ttttgat putative branch site (score: 4)
tttgttttgtttcc CT-rich tract
tttgaatatgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA