Sequence
atgc intronic sequence ATGC exonic sequence...tgtttttcatacagcattcatagttgtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
Basic information
| species | Glycine max |
| transcript | GLYMA18G45340.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtttttcatacagcattcatagttgtgtggctgaggct---gtcttgattgtcacttaatatactctttatattttatatctaattgctatattcct-catagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
|| | | || | || || || || | | | | || | | | | | | || | || ||||| | | | ||| || | ||||||||||||||| || |||||||| |||||||| || ||||||||| | || ||| | ||||||| || || ||| | | |||||||| ||||||
-gtatgttatgtccc-ttgatgcttcgctgtttaaagtttaagtttcgttca--ggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG
upper sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------tgtttttcatacagcattcatagttgtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgct--atattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
| ||| | | | || || || || | | | || | | | || | || || || || | ||| || || | || | ||||||||||||||| || ||||| ||||||||||| || ||||||||| | | || || | ||||||||||| |||||| | | || ||||| ||||||
gtatgatctaatatcttgttgtggcttatctttacgccctgaatctatttattttgtggtat-cagagctgcgatcattaactagtgcgaactat---ttgaagtagcattcat-ttctgtattggttttcttgaccttgtttttagGATGGTCAATGGTCTCCTTAAGACTGCTCAAGGAGTGCCTCCTGGTACAGTTACTACCTTGTTGCCACCTCAGGAAGCAGCCATGAAGCTTGAAGCCATG
upper sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 2
tgtttttcatacagcattcatagtt----gtgtggctgaggctgtcttgattgtcacttaatatactcttta-tattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
||||||| | | | | || ||| || ||| |||| || || | | | || |||| || | | | | | ||| | || || || ||||||||||||||||||||||||||||||||||||||||| || || || ||||| || ||||||||||||| || | |||||||| || |||
-gtttttc-ttctgtcctaatggttttgagtatggttgag-ttggctaaggtttaaatttttatatgggttggtgtccttcacttcattattg--ttacttccagAATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCAGGCGTTGCCACTACACTGTTACCACCTCAAGAAGTGACCATGAAACTTGAAGCTATG
upper sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15473 (Selaginella moellendorffii), 3'ss of exon 2
tgtttttcatacagcattcatagttgtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
| || || ||||| | | || |||| | ||| | ||||||| ||| |||| |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
-----------------------------------gtatgcctcgattga-attcaa---gttcttcg---ctgata---atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG
upper sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 2
tgtttttcatacagcattcatagttgtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
| || || ||||| | || || |||| | ||| | ||||||| ||| |||| |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
-----------------------------------gtatgcctcgattg--aatt--catgttcttcgc---tgata---atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtcacttaatatactctttatattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
atctaat putative branch site (score: 3)
tattcctc putative PPT
ttaatatactctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttttcatacagcattcatagttgtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgctatattcctcatagGATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - tcataca
- - - - - - -gcattca
- - - - - - - - - - - - tgtgtgg
- - - - - - - - - - - - - - - - - aggctgt
- - - - - - - - - - - - - - - - - - - - - - - -tgtcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctata
