Sequence
atgc intronic sequence ATGC exonic sequencegtgtggagaacagcatcatgaaagtctttgattatattccaaaatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
Basic information
species | Glycine max |
transcript | GLYMA20G28410.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 4
gtgtggagaacagcatcatgaaagtctttgattatattccaaaatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
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----------------------------------------gtaaggcgtctctgattg-gctagatagtgctactggattgtgctcgtgatcccaatttgcagtagttttacgggaatttgattggggtggaggtgtgggattgtttggtt--agGCACGCCGGAGTTCATGGCGCCAGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATATACTCGTTCGGGATGTGCGTGCTTGAGATGGTCACCTT
upper sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034779_T01 (Zea mays), 3'ss of exon 4
gtgtggagaacagcatcatgaaagtc-tttgattatattccaaaatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaa-gactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
| ||| | | |||||| | | | ||| ||||| || | || | | | || || | | || | ||||| | || ||| || || || ||| | ||| ||||| ||||| ||||| || || |||||||||||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | ||||||||||| ||
-------------------gtaagccatctgattagctcactagcccgaaatt-----atgttgtttgatc-----acaactgg----caatagctactcggt-----aatttaatggggctagatgtg--------tcggattggttggat---agGTACACCGGAGTTCATGGCACCGGAGGTGTATGAAGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTCACCTT
upper sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089159_T02 (Zea mays), 3'ss of exon 4
gtgtggagaacagcatcatgaaagtctttgattatattccaaaatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
| | || | || |||| | | | |||| ||| | | | | | | | | | || |||| | || | || | | | || ||| || || ||| || ||| ||||| ||||| ||||| || || ||||| || ||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | |||||||| || ||
-------------------gtaggtaatccatctgattc--gcacactagcgagaaa---ttatgttgcccgatcactactgg----caatagctgcgcggtg----atttgatggcgctagatgtgtcggatcg--------gttggac---agGTACACCGGAGTTCATGGCGCCGGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTAACGTT
upper sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 4
gtgtggagaacagcatcatgaaagtctttgattatattccaa--aatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
|| |||| || | | | | | | | | ||| | || | | || |||| | || | || | | | || ||| || || ||| || ||| ||||| ||||| ||||| || || ||||| || ||||| ||||| ||| |||| ||||| ||||| |||||||||||| | | |||||||| || ||
---------------------------------gtaatccatctgattcgcacactagcgagaaattatgttgcccgatcacta-ctggcaatagctgcgcggtg----atttgatggcgctagatgtgtcggatcg--------gttggac---agGTACACCGGAGTTCATGGCGCCGGAGGTGTACGAGGAGGAGTACAACGAGCTGGTGGACATCTACTCGTTTGGAATGTGCGTGCTCGAGATGGTAACGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
tcttgat putative branch site (score: 4)
tttgcttattcttctt CT-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtggagaacagcatcatgaaagtctttgattatattccaaaatatgaatatgaaaatgttacttatctctttgataattagttctccatctctgcacagtttaccagtttaagactcttgatttgcttattcttcttctttgttttactccagGCACACCTGAGTTTATGGCTCCAGAAGTGTATGAAGAGGATTACAATGAGTTGGTTGACATATACTCTTTTGGAATGTGCATCTTAGAGATGGTCACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG