Sequence
atgc intronic sequence ATGC exonic sequence...cattagtaatctttttttagcacttcttttgccttaactgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
Basic information
species | Glycine max |
transcript | GLYMA05G31920.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g33490.1 (Oryza sativa), 3'ss of exon 1
cattagtaatctttttttagcacttcttttgccttaac------tgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatattt-cagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
| | | ||| || | |||| | || ||| || | || || | | | || |||| |||| | | || | ||||||||||||||||| ||||| || || |||||||| ||||| |||||||| || ||||| ||||| | ||||| | || || || ||| || ||
-------attgtgtttctaagcaccttcttgcttaaataagtcatgtgtttccaatatttaaatctggagatcttcttctcttaaatctgattgttaacatctgcagAGCTGGGAGAAAACGATGGACTGCCACAGTCCAGGTCAAGGGTTGATGCCAGCAAGTTTCAAGGTGCGTGTTGTTCCACTTGACGGGGACGATGATGTAA
upper sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g32730.1 (Oryza sativa), 3'ss of exon 2
cattagtaatctttttttagcacttctt-ttgccttaactgtattat-aattactttgttgtttctga--tatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
||| | || | ||||| || || || | | || |||| | || | || | | || || || | ||| | ||||||||||||| || ||||| || |||||||||||||| || || ||||||||||| || ||||| | ||| |||| | ||||| ||||| |||||
---aagttcttggcaaatatctcttctagttaccgtagcaacaaaatgaatttgtatgccctatccaaggtgtaacaagttctgctgtcattttgttatgt-agAGCTGGGAGAAGACAATGGACTGCCATAGTCCAGGACAGGGCTTAATGCCTGCTAGCTTCAAGGTGCGAACAATTCCACTCGATGGAGATGAAGATGCAA
upper sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G040843_T01 (Zea mays), 3'ss of exon 2
---catta-gtaatctttttttagcacttcttttgccttaactgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
|| |||| | | | |||| || | | | ||| | ||| | | || ||||| | |||||| | | | | | |||||||||| ||||| ||||| || ||||||||||| |||||||| ||||| || || || || || ||||| |||| | ||||||||||| |||||
taaagctacaaaatcctgaatcaccactaaatt-gagtgacatgtcctg-aatgattcccctggatctgacagtttgtctgacaccttgag--ctggtctgtagAGCTGGGAAAAAACAATGGACTGCCATAGTCCAGGTCAAGGTTTAATGCCCGCCAGCTTCAAAGTGCGGACAATTCCACTTGATGGTGATGAGGATGCAA
upper sequence: GLYMA05G31920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0074g00720.t01 (Vitis vinifera), 3'ss of exon 3
cattagtaatcttt-ttttagcacttctt--ttgccttaactgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
|| | |||| || || | || | || ||| ||| || ||| | ||| || || | | | | | ||| | |||||||||||||| || ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||| | |||||||| ||||||||||||| |||||||
gatgattaattattaccctaactatttatcatttactttacttccttttaaacatggagtttatttgcccatttgggcacgtttgtg---gctcatcctgcagAGCTGGGAGAAGACAATGGACTGTCATAGTCCTGGTCAAGGGTTGATGCCTGCAAGTTTCAAGGTGCGCACAGTTCCCCTGGATGGTGATGACTCTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
ttctgat putative branch site (score: 3)
tgatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattagtaatctttttttagcacttcttttgccttaactgtattataattactttgttgtttctgatatattgtcttgaatccacacatccatatttcagAGCTGGGAGAAAACTATGGATTGTCATAGTCCAGGACAAGGTTTGATGCCTGCTAGTTTTAAGGTTAGGACAGTTCCTTTGGATGGTGATGATTCTGCAA
- - - - - - - - - -gcacttc
- - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacaca