Sequence
atgc intronic sequence ATGC exonic sequence...ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttttgtcatgctggcattatagcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
Basic information
| species | Glycine max |
| transcript | GLYMA19G04970.1 |
| intron # | 12 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G04970.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G344967_T01 (Zea mays), 3'ss of exon 16
ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttt-tgt-catgctggca----ttatagcttatacaacttattgatt-tctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
| || || | || | | | |||| | | | ||| ||| | | | |||| || ||| | | | || | || | ||||||||||| | | || |||| ||||| || |||||||| |||||||| |||||||||||||| ||||| ||||| |||||||| |||||| |
-------gtaaatgatatgttgtcacttctcaatgacttgggcattattctatttatatgcttgctaccagctgttaaatcactgatcttttgtcaataatttgcagTGCTACTCTCCAGACCCTCAAATAGCAGATGGCTATTTCAGTGTTCTGGCTGAAGTCTACATGCGCCAGGAGATTCCAAAATGTGAAATCCAGAGACTTG
upper sequence: GLYMA19G04970.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 17
ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttttgtcatgctggcat-tatagcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
| || | || | | ||| | || | | | | | || | || | || | || | | | ||| ||||| ||| ||||| || | || |||| ||||||||||||||||| |||||||||| |||||||| ||||| |||||||| |||||||| ||||| | |
ataagcttttttcacttctatgctttgctcatctgtttgactacatccttgattagactcttctaaactgcatgacctaattcatctgt-acttttcccagTGTTACTACTCTGATGCGGCTATAGCTGATGGGTACTTCAGTGTGTTGGCTGAGGTTTACATGCGACAAGAAATACCAAAATGTGAAATCCAGAGGCTCT
upper sequence: GLYMA19G04970.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0083g00750.t01 (Vitis vinifera), 3'ss of exon 16
ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttttgtcatgctggcattat----agcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
||||| | | ||| | | | ||||| || | | | || |||||| || || | | | || | ||| | ||||| ||||||||| | ||| || || | |||| ||||| ||||||||||| |||||||| ||||| |||||||| || || ||||| |||||||| |||||| |
ctgctact----ttgtttgcttggtatcttattcctgtcattaattttcaacttttgtaatacttatcatgttcagggagtaattagcttcatattttcttcagTGCTACTATTCTGATGCTGCGATAGCTGATGGCTACTTCAGTGTGCTGGCTGAAGTCTATATGCGCCAGGAAATTCCAAAATGTGAAATTCAGAGACTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctgttttgtcatgctggcattatagcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
tattgat putative branch site (score: 3)
tttctgc CT-rich tract
ttatacaacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcttttcagataattttttccttgtattatttctcttgtggagttatctgttttgtcatgctggcattatagcttatacaacttattgatttctgcagTGCTACCACTCTAATTCTTCTGTAGCCGATGGGTACTTCAGTGTACTGGCTGAGGTCTACATGCGCCAAGAGATACCAAACTGTGAAATACAGAGATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
ctgcttt
- - - - - - - - - - -ccttgta
- - - - - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
