Sequence
atgc intronic sequence ATGC exonic sequence...cccgaagcttacatttttatgtgatttaaatttctgaacattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 5 |
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 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
---cccgaagcttacatttttat-gtgatttaaatttctgaacattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
| | | || | || || ||| || || | | | |||| ||| ||| | | || | |||| |||| | |||| |||||||| || || ||||| |||||||| || |||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||||
atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgt---tctatatcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
---cccgaagcttacatttttat-gtgatttaaatttctgaacattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
| | | || | | || || ||| || || | | | |||| ||| ||| | | || | |||| |||| | |||| |||||||| || || ||||| |||||||| || |||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||||
atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgt---tctatatcatcctaacattgatgtgctctctttttcacccat-cagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
cccgaagcttacatttttatgtgattta--aatttctga--acattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA-
| || | | ||| ||| | | | |||| | | ||| | || |||| ||| | | | | | | | ||| ||||| ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || ||||| |||||||
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttg---tatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
cccgaagcttacatttttatgtgattta--aatttctga--acattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
| || | | ||| ||| | | | |||| | | ||| | || |||| ||| | | | | | | | ||| ||||| ||||||||||||| || || ||||| |||||||| || ||||| ||||| || ||||| ||||| |||||||| ||||| || || ||||| |||||||
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttg---tatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
cccgaagcttacattttta-tgtgatttaaattt--ctgaacattaa-accttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
| | | |||| | || | || || | | |||| | | || |||| | | | || |||| | | | ||||||||| |||||||| || ||||| || |||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| |||||| |
---aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaaca-atgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
cccgaagcttacatttttatgtgatttaaatttctgaacattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgt--ttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
| ||| | || || | || || || | | | || ||| | |||||||| || |||||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||| || || |||||||| |
---------------------------------------------------gtatccatttct-tgaaaagtttcttgtagctaacaaagaaactcttttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
tattaat putative branch site (score: 2)
ttttgttt putative PPT
ttattaatgtgtaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccgaagcttacatttttatgtgatttaaatttctgaacattaaaccttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - gcttaca
- - - - - - - - - - - - - - - - tctgaac
- - - - - - - - - - - - - - - - - - - - - - -ccttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaataa