Sequence
atgc intronic sequence ATGC exonic sequence...tacataaaattgctggtttgtttctttgaattacctgaatcagttcaaattcatattttaaatgcacatttatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
Basic information
species | Glycine max |
transcript | GLYMA18G46480.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
tacataaaattgctggtttgtttctttgaattacctgaatcagttcaaattcatattttaaatgcacatt-tatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
| | |||| |||| || | | || || | | || || | | |||| | ||| | || | |||||||||||||| || || | ||| | ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| ||||| | ||||| |||
-------gtcttttactttgcttctccaccttccttc--tctactctagct-atcttct---tcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g03190.t01 (Vitis vinifera), 3'ss of exon 2
---tacataaaattgctg--gtttgtttctttga-attacctgaatcagttcaaatt-catattttaaatgcacatttatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
| || || ||| ||||| || ||| ||| |||| |||| ||| ||| || | || | || ||| ||||| | || ||||||||||||| || |||||||| | || || || || || |||||||| |||||| ||||||||||||||||||||||||| || | |||||||||
ctttggttaggttttctgcaatttgtcactctgacattgatggaatattttcatatttcatgttatgaacttttaacaat-acttgatacact------atgttcagGTGGGCTGCCATTGCCTCTCAACTGCCCGGAAGGACCGATAATGAGATCAAGAACCTATGGAACACCCACTTGAAGAAGCGCCTGCTTGGAATGGGGCTT
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
tacataaaattgctggtttgtttctttgaattacct---gaatcagttcaaattcatattttaaatgcacatttatgact--atatacattga-acaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
| || ||||||| |||| || | | | || | | | | | | | | ||| || | || ||| |||| ||| ||| |||| ||||| || | || | | || ||||| ||||| ||||||| |||||||| ||||||||||||||||||| ||||| ||
------tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaaattgattttttggaatgtgttgttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------tacataaaattgctggtttg---tttctttgaattacctgaatcagttcaaattcatattttaaatgcacatttatgactatatacattgaacaaattct-cagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
| ||| | | | | || | | | ||| | || ||| | | | | | ||| || | |||| || | ||| ||| | || ||||| ||| | || | | || ||||| |||||||| |||| |||||||| ||||||||||||||||| |||||| ||
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaattcatattttaaatgcacatttatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
ttctc CT-rich tract
atattttaaatgcaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacataaaattgctggtttgtttctttgaattacctgaatcagttcaaattcatattttaaatgcacatttatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - tgctggt
- - - - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcac