Sequence
atgc intronic sequence ATGC exonic sequence...cagcattgtcaccatttcattacagtgaccccattgtgaagtttccacattttttttgtgtttctattttttttatgtgagattcggcgttcttttgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------------cagcattgtcaccatttcattacagtgaccccattgtgaagtttccacattttttttgtgt--ttctatttttt----ttatgtgagattcggcgttcttttgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
| ||||| | | | || |||||| |||| ||||| || | || | | || || ||| | ||||| | || |||| || || | ||||| | | ||||||||| |||||||| |||||||| ||||| ||||||||||| |||||||| ||||| || | || |||||||
gtaagttctggagctcgatttgttcgttattgtttaaattcacttcagttcgtagtagatcttggattgttctggatctgtgttacagat--cattgttgagttagttgttttttagtggataattttggtgttgattgttctgtttggttcggtggaatt--gcagTTGTCTAGTATCGGAATTAGTCCGCAATTCATGACATTTACGCATGTGACCATGGAGTCGGATAAGTATATTTGTGTTAGGGAGACGGCGCCGCAGAACA
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 1
cagcattgtcaccatttcattacagtgaccccattgtgaagtttc-cacattttttttgtgtttctattttttttatgtgaga---ttcggcgttcttttgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
| | ||| | | || | | ||| ||||| | | | | | | | | | |||| || | | ||| |||||||| ||| | || || |||||||||||| | |||||||| |||||||| ||||| || ||||| |||||||| || |||| || || || ||||
ggggagtgtggggctgttg----agaggtggaacggtggagtttgatagagtggacattggatgaagtgctgatggtgtgggagaatgggatgttgcaatgcagCTGACGAGCCTCGGGATTAACCAGCAATTCGTCACATTTACACATGTGACGATGGAGTCCGATAAATACATTTGCGTGCGGGAGACGTCGCCGCAAAACA
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 1
cagcattgtcaccatttcattacagtgaccccattgtgaagtttccacattttttttgtgtttctattttttttatgtgagattcggcgttcttt----tgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
| || | || | | | || | | | ||| ||| | | ||| |||| || | | | ||||||| ||| | || || ||||| |||||| | |||||||| |||||||| |||||||| || ||||||||||| || |||| ||| ||||||||||
--gggaggtggctatgtaagttt--cgattttggctgcagttaactttgtttgcagagtggtatactagagttttgctgagctttgctaattctggcaatgcagCTTACAAGTCTGGGCATAAACCAACAATTCGTGACATTTACACATGTGACGATGGAATCCGACAAGTACATTTGCGTGCGGGAGACTTCTCCTCAGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattttttttgtgtttctattttttttatgtgagattcggcgttcttttgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
cgttctttt CT-rich tract
tttttttgtgtttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagcattgtcaccatttcattacagtgaccccattgtgaagtttccacattttttttgtgtttctattttttttatgtgagattcggcgttcttttgcagCTGGGAAGCGTTGGAATCAACCAGCAATTCATTACATTTACTCATGTGACAATGGAATCGGATAAGTACATTTGTGTCAGGGAAACTGGACCTCAGAACA
- - - tgtcacc
- - - - - - - - - - tacagtg
- - - - - - - - - - - - - - ccccatt