Sequence
atgc intronic sequence ATGC exonic sequencegtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
Basic information
species | Glycine max |
transcript | GLYMA01G34560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------gtgtggctgaggctgtcttgattgtcactta-----atatactctttatattttatatctaattgttatattcct-cataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
| | |||| || | | || | | | | || | || ||||| | | | ||| || | || |||||||||||| || |||||||| |||||||| || ||||||||| | || ||| | ||||||| || || ||| | | |||||||| ||||||
gtatgttatgtcccttgatgcttcgctgtttaaagtttaagtttcgttcaggtggaagttctttgcgtaatttatgtttcctctgtatgatcatgtttagGATGGTCAATGGTCTCCTTAAAACGGCTCAAGGGGTTCCTCCTGGTACAGCTACAACATTGATGCCACCACAGGAGGCAGCTATGAAACTTGAAGCCATG-
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------gtgtggctgaggctgtcttgattg--tcacttaatatactctttatattttatatctaattgtt--atattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
| | || | || | | | || | || || || || | ||| || | | || | || |||||||||||| || ||||| ||||||||||| || ||||||||| | | || || | ||||||||||| |||||| | | || ||||| ||||||
gtatgatctaatatcttgttgtggcttatctttacgccctgaatctatttattttgtggtatcagagctgcgatcattaactagtgcgaactatttgaagtagcattcat-ttctgtattggttttcttgaccttgtttttagGATGGTCAATGGTCTCCTTAAGACTGCTCAAGGAGTGCCTCCTGGTACAGTTACTACCTTGTTGCCACCTCAGGAAGCAGCCATGAAGCTTGAAGCCATG-
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtgtggctgaggctgtcttgattgtcacttaatatactcttta-tattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
|| ||| |||| || || | | | || |||| || | | | | | ||| || | | || | ||||||||||||||||||||||||||||||||||||||||| || || || ||||| || ||||||||||||| || | |||||||| || |||
gtttttcttctgtcctaatggttttgagtatggttgag-ttggctaaggtttaaatttttatatgggttggtgtccttcacttcattattgt--tacttccagAATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCAGGCGTTGCCACTACACTGTTACCACCTCAAGAAGTGACCATGAAACTTGAAGCTATG-
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15473 (Selaginella moellendorffii), 3'ss of exon 2
gtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
| || || ||||| | | || |||| | ||| | ||| ||| ||| || | |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
----------gtatgcctcgattga-attcaa---gttcttcgc---tgata---atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG-
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 2
gtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
| || || ||||| | || || |||| | ||| | ||| ||| ||| || | |||| |||||||| |||||||||||||||||||| ||||| || || || || | || ||||| || | | || |||| || |||
----------gtatgcctcgattg--aatt--catgttcttcgc---tgata---atttgctattttc----tagGCTGGTAAATGGACTACTTAAAACTGCTCAAGGTGTACCTCCGGGCGTGGAGAGCAGTTTGACTCCTATCCAAGATGCCGCTATGAAGCTTGCTGCAATG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtcacttaatatactctttatattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtggctgaggctgtcttgattgtcacttaatatactctttatattttatatctaattgttatattcctcataagATGGTCAATGGACTTCTTAAAACTGCTCAAGGTGTCCCTCCTGGTGTAATGACCACACTTTTGCCACCTCAAGAAGCAACATTAAAACTTGAGGCCATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA