Sequence
atgc intronic sequence ATGC exonic sequencegttagtaatatctccatcacgtgcacaaatattccttttcttgatattttttcttttaaatgttgctgaaaagtctccatatttcagAGTAAGGGCCATTTACACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
Basic information
species | Glycine max |
transcript | GLYMA11G04490.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04490.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G033526_T01 (Zea mays), 3'ss of exon 11
-----------------------------------gttagtaatatctccatcacgtgcacaaatattcctttt-cttga-tattttttctttt-------aaatgttgctgaaaagtctcc-------atatttcagAGTAAGGGC--CATTTACACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
|| | | | | ||||| | ||| || | |||| ||||| |||||| | ||| | || || |||| | || || || | || ||| | || | | ||||| | | || ||||||||||| || |||| |||||||| |||||||||||||||||||||| ||||| | |
gtaagaccatgtgctgtgaagttccattactgaccttttgcagtcagttcatcagataaacacatctctgttttacttgaatattttgcccttttgttattatattttactgattattcgtggattggaatgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA
upper sequence: GLYMA11G04490.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------gttagtaatatctccatcacgtgcacaaatattccttttcttgatattttttcttttaaatgttgctgaaaagtctccatatttcagAGTAAGGGCCATTTAC--ACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
| || | ||||| | | || | |||| |||||| |||||| || | | | | | || | | || ||| | || | | ||||| | | || ||||||||||| || |||| |||||||| ||||||||||||||||| |||| ||||| | |
gtaaggccattgtgctgtgaagtttcactgctgatcttttgcagtcagttcatcagataaacacatctcggctttacttg-atctttttttgctcttccgtttttttattttaactgattattcatggattgaatgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA
upper sequence: GLYMA11G04490.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 11
gttagtaatatctccatcacgtgcacaaatattccttttc--ttgatattttttctt-ttaaatgttgctgaaaagtctccatatttcagAGTAAGGGCCATTTACACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
|||||| | | || | || || | | || || | || |||| ||| || ||| | | ||| | | ||| ||||||| | | |||||| ||||||| ||||||||||||||||||||||||||||||||||| | ||||| ||||||||||| ||||||||||
gttagtgtttttcttatttttttcattctctttatgctcagatcattacttcatgttgttaagtgt--ctccaaatttttcatgtgt-agAACAAGGGCCTAATGAAGGAGGGAGAGCATGTGACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGTGTTGAATCTACTCACCACATCCAAGTTCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttttcttgatattttttcttttaaatgttgctgaaaagtctccatatttcagAGTAAGGGCCATTTACACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
tcttgat putative branch site (score: 4)
tctccat putative PPT
ttcttgatattttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaatatctccatcacgtgcacaaatattccttttcttgatattttttcttttaaatgttgctgaaaagtctccatatttcagAGTAAGGGCCATTTACACGAGGGACAGCATGTTACTCTTGTTCAAAGTGGAGCACAACCAATCTGGCGAGAGGAATCCACTCACCACATACAAGTTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA