Sequence
atgc intronic sequence ATGC exonic sequence...atagtcacattgtttagactatacagtactgctcttgtataaatattgtgataatggtgattttattgatctttgtaaaaatgttgtgcttcttgggcagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
Basic information
species | Glycine max |
transcript | GLYMA18G49960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15470.1 (Arabidopsis thaliana), 3'ss of exon 3
atagtcacattgtttagactatacagtactgctcttgtataaatattgtgataatggtgattttattgatctttgtaaaaatgttgtgcttcttgggcagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
|| | | | || | |||||| | | ||||| | |||| | || | | | ||||| |||||||| || ||| | || || || || || ||||||||||| || ||||| || ||||||||||||||||| || || ||||| ||||||||||| |
atttggaagagatctttgttaattcttgttgctctctaaagtgagccatatcaatgggaagattatcatatgtgatatatctctatcttgtcttgaacagATGGAGAAGTTTGAACGTGATATGAGGGAATCGAAATTTGCAGAACTTATGAACAAGCACTTTGCAGCAAGTTCCATTCCCAAAGGCATTCATTGTCTCT
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01040.2 (Arabidopsis thaliana), 3'ss of exon 3
atagtcacattgtttagactatacagta-ctgctcttgtataaatattgtgataatgg--tgattttattgatctttgtaaaaatgttgtgcttcttgggcagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
|||| | || |||| ||||| | || | | |||| | | | | | | || ||| ||| ||| | || || ||| || || | || || || ||||||||||| || ||||| || |||||||| |||||||| || || ||||| ||||| ||||| |
--------------------gtacattctctaatcttcaataaaagcttaaattgtagattgatccgaaacttatatttgatttgattactctttttgaacagGTAGAGAAGTTTGAAAGGGATTTAAGGGAATCCAAATTTGCAGAACTCATGAACAAGCACTTTGCTGCAAGTTCAATTCCAAAAGGAATTCACTGTCTCT
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 3
atagtcacattgtttagactatacagtactgctcttgtataaatattgtgataatggtgattttattgatctttgtaaaaatgttgtgcttcttggg-cagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
|| | || |||| | | | | | |||| | || | |||| | | || ||||| | | || ||| |||||||| || | ||| || || ||||| || || || |||||||| |||||||||||||||||||||||||| | || || ||||| ||||| |||||||
ccagagattttttttaaccatttcctaaaagatcttaga-gcctaacccaactctggttttaattaatatgtttgtttctctctctctctctctggctcagATGGAGAAGCTTGAAAGGGATATCAGGGAATCAAAGTTTGCAGAATTGATGAATAAACACTTTGCAGCAAGTGCCATTCCAAAAGGCATTCACTGTCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgataatggtgattttattgatctttgtaaaaatgttgtgcttcttgggcagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
tattgat putative branch site (score: 3)
tgcttctt putative PPT
attttattgatctttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtcacattgtttagactatacagtactgctcttgtataaatattgtgataatggtgattttattgatctttgtaaaaatgttgtgcttcttgggcagATGGAAAAACATGAGAGAGAAATCAGAGAGTCTAAATTTGCAGAGCTGATGAATAAACACTTTGCAGCAAGTTCTATCCCTAAAGGGATTCATTGTCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - ctgctct
- - - - - - - - - - - - - - - - - - - - - - - - - - aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg