Sequence
atgc intronic sequence ATGC exonic sequence...ttatcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttagcacacaaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
Basic information
species | Glycine max |
transcript | GLYMA11G14020.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14020.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G12950.1 (Arabidopsis thaliana), 3'ss of exon 7
ttatcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttagcaca-caaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
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--------------------gtaggattttaaacttttccccctctttctatttgctcaaggt---aacatactaacatatcaacacttgtacaatttcagGTCTCTAGGAATCTGTTCAGATGGACAAAAGAGGTTAGCTATGCAGACTATTACGAGCGCGCCTTGACCAACGGCGTGTTGGGAATTCAAAGAGGAACCC
upper sequence: GLYMA11G14020.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G12960.1 (Arabidopsis thaliana), 3'ss of exon 7
ttatcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttagcacacaaaaa-taaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
| | || | | ||| | | | | | ||| | | | | || || | | | | | ||||||||| || | | ||||| |||||||| ||||| || ||||||||||||||||||||||| || ||||| ||||||||| | |||||||||||||| |
---------------gtaggatttcaaacttccc---cacacccccacccccctcttttcatttgc-tcaacgtaacatattgacacttgtacaatttcagGTCTCTAGGAATCTGTTCAGATGGACAAAAGAGGTTAGCTATGCAGACTATTACGAGCGCGCTTTGACCAACGGTGTGCTCGGAATTCAAAGAGGAACCG
upper sequence: GLYMA11G14020.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g01650.t01 (Vitis vinifera), 3'ss of exon 7
----tta-tcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttagcacacaaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
| | ||| || || | | || || ||| ||||| | || | | || ||| ||| | | | | ||| || || ||||||| ||| |||| ||||| ||||| |||||||| | ||||| || ||||||||||| ||| | || ||||| | | |||||||||||||||||||
tttttcactcaaaccagcataaaactcttagtgctctgcattttta--tgcacgcattgaaatttggttctgtaggact--tttgctgagatatgatt-ttgtagGTTTCCCGCAACCTCTTTAGGTGGACAAAAGAAGTGGCATATGCCGATTATTACGAGCGAGCCCTGACAAATGGCATTTTAAGCATTCAAAGAGGAACAG
upper sequence: GLYMA11G14020.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g01770.t01 (Vitis vinifera), 3'ss of exon 7
---ttatcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttag-cacacaaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
|||| | | | || || || | || ||||| ||| || | | | | | |||| || | || || | || || || |||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||||||||| | || |||||||| | ||||| |||||||||||||
tttttattatgaacgtgtagctcaaggcgtgatttttatttatatcaccataaaagtct---tctcttcattttcaaggacaaactgacatttgatt-ttgtagGTTTCGCGCCACCTCTTTAGATGGACCAAAGAAGTGGTATATGCAGATTATTATGAGCGCGCCCTGACAAATGGTGTTTTGAGCATCCAAAGAGGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgtttgtgattgtttccattatcttagcacacaaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
acaaaaataaaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcacacagtaattcatcgctgcatgttcttcatttacatctgtatgtgtttgtgattgtttccattatcttagcacacaaaaataaaatgatttcagGTTTCGCGCCACCTGTTTAGATGGACCAAAGAAGTCTCTTATGCAGACTATTACGAGCGCGCCTTAACCAATGGTGTGCTCAGCATTCAAAGAGGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - cacacag
- - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - cttcatt
- - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa