Sequence
atgc intronic sequence ATGC exonic sequencegtgagtagaacggcatcatgaaaaccttttgattatattccaaaagatgaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
Basic information
species | Glycine max |
transcript | GLYMA10G39390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 4
gtgagtagaacggcatcatgaaaaccttttgattatattccaaaagatgaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaa--gactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
||| | | ||| | | | || ||| ||| || | | |||||| | | |||||| | | | | | ||| | |||||| || ||||| ||||| ||||| ||||| || ||||| ||||| ||| |||| ||||||||||| || || |||||| | | ||||||||||| ||
-----------------------------------------gtaaggcgtctctgattggctagatagtgctactgg--attgtgctcgtgatcccaatttgcagtagttttacgggaatttgattggggtggaggtgtgggattgtttggtt-agGCACGCCGGAGTTCATGGCGCCAGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATATACTCGTTCGGGATGTGCGTGCTTGAGATGGTCACCTT
upper sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G034779_T01 (Zea mays), 3'ss of exon 4
gtgagtagaacggcatcatgaaaaccttttgattatattccaaaagatgaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
| || || | |||||| | | | |||| | | | |||||| | ||| | || || | | || | | | | || ||| || || || ||| | ||| ||||| ||||| ||||| || || |||||||||||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | ||||||||||| ||
-------------------gtaagccatctgattagctc-------actagcccgaaattatgt------tgtttgatcacaactggcaatagctactcggtaatttaatgggg---ctagatgtg--------tcggattggttggat---agGTACACCGGAGTTCATGGCACCGGAGGTGTATGAAGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTCACCTT
upper sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089159_T02 (Zea mays), 3'ss of exon 4
gtgagtagaacggcatcatgaaaaccttttgattatattccaaaagatgaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
| | || || | ||||| | | || ||| ||||| | ||| | |||| | || |||| | || | | | | | | || ||| || || | ||| || ||| ||||| ||||| ||||| || || ||||| || ||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | |||||||| || ||
---------------gtaggtaatccatctgattcgcacactagcgagaaatt-----atgttgccc--------gatcactactggcaatagctgcgcggtgatttgat---ggcgctagatgtg--------tcggatcggttggac---agGTACACCGGAGTTCATGGCGCCGGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTAACGTT
upper sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 4
gtgagtagaacggcatcatgaaaaccttttgattatattccaaaagat--gaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
|| |||| ||| | | | | | | | | ||| | |||| | || |||| | || | | | | | | || ||| || || | ||| || ||| ||||| ||||| ||||| || || ||||| || ||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | |||||||| || ||
----------------------------------gtaatccatctgattcgcacactagcgagaaattatgttgcccgatcactactggcaatagctgcgcggtgatttgat---ggcgctagatgtg--------tcggatcggttggac---agGTACACCGGAGTTCATGGCGCCGGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTAACGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
tcttgat putative branch site (score: 4)
tgcttcttctttgttt putative PPT
tttgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtagaacggcatcatgaaaaccttttgattatattccaaaagatgaatatgaaaatgttccttttctctttgataattactctccatgtctgcacagttactagtttaagactcttgatttgcttatgcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG