Sequence
atgc intronic sequence ATGC exonic sequence...acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcattatgttgaactgttttgattaaacctaatatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
Basic information
species | Glycine max |
transcript | GLYMA02G05440.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 7
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcattatgttgaactgttttgattaaacct-aatat-ttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
| | | || | | | ||| | || | || | | || | | || | | ||||| || ||| | | |||| || ||| ||||||||||| ||||||||||| ||||||| ||||| ||| ||||||||||||| | ||||||||| |||||||| || || || || | ||
-gtaagttcctacatctaatctaagatagtcttaatacaatagtagtgaatcttcgtcagctgtcaatccttactgtcctgtttatgctttgatatgtttagCGCATCCATGGGTAAGAGAAGGAGGAGAAGCATCTGAGATCCCTGTTGATATATCTGTATTGTCCAACATGCGTCAGTTTGTCAAGTACAGCCGTTTTAA
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 7
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcattatgttgaactgttttgattaaacctaatatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
| || | || || | |||| | || | | || | | | || || || | | | | | |||||||||||||||||||||||||||| || |||| |||||||| || || |||||||| || | ||||||||| ||||||||||||| ||| || | ||
-------------gtaagcgttttgacaccattttaaatcattttgttcttatcttttctgatctttctgtaaggattgtggattttcttggt--tgcagCACATCCATGGGTTAGAGAAGGAGGAGATGCATCTGAGATTCCCATAGACATATCTGTTCTGAACAACATGCGTCAGTTTGTGAAATTTAGCCGCCTTAA
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 7
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcattatgt-tgaactgttttgatta--aacctaatatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
| | |||| || |||| | | | ||| | | | | ||| | | | | | | | ||| | | | || ||||||| ||||||| | |||||||||||| || | ||| |||| || || |||||||| || | ||| ||||| ||||||||||||| || || ||||
----------------gtatgttatgcacaagcaaatgc-catatatttccattatttttggttaacttataagttactcaacttatggatttggt-ttgtagCACATTCATGGGTGAAAGAAGGAGGTGAGGCCTCAGAGGTTCCAATAGACATATCTGTTCTTAACAATATGCGTCAGTTTGTGAAATTCAGCCGTCTGAA
upper sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcat-tatgttgaactgttttgattaaacctaa-tatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
||||| | | | | | || | | | ||| | ||||| | ||| || | | || | | | ||| | ||| | ||||||||||||||||||||||||||||||| || || | |||||||| |||||||| ||||| || ||||||||| | ||||| || || |||| ||||
ggttattatatgtgatctatgttggac-tgttatggtttgcctctatgt-tttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgtaattgtgttgcattatgttgaactgttttgattaaacctaatatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
acctaat putative branch site (score: 3)
ttttgattaaacctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcattatgttgaactgttttgattaaacctaatatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg