Sequence
atgc intronic sequence ATGC exonic sequence...gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
Basic information
species | Glycine max |
transcript | GLYMA16G05460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
gtttgaggtctgtttcatttgcatcttataacttgatatata-aaaggtcctgatacctgataatatgacctgtataac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|| | | || | | || | || || | || | | || | | | || | || | | | || || ||| || || |||| || |||||||||||||| || ||||||||||||||||| ||||||| |||||||| | || || ||| |||||||| ||| | ||| |
---tggcatg-gcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 3'ss of exon 3
---gtttgaggtctg-tttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
| ||| | || | |||| | | ||| | ||| | | ||||| | || | ||| ||| |||| | | |||| ||||||||||||||||| || ||||||||||||||||| | ||||| ||||| || | || || ||| ||||| | |||| | || |
tctggttgttttttggtatcataagaaatatatcttgccaaataccttctctatttctacctttagacattattattatttt-taataatgatatact---cagATACAATGATGAAGTTTGCATCCTTTGAGACCATTGTTGAACAAATCTACAAGCATGCTGTTCCTGTCCCGAAGTCAGAGTGTAGCAAATCATTCCAGTT
upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacct-gtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| ||| | || | | |||| || | || | | | | |||| ||| || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || | || || ||| |||||||| ||| || |
aatttggtagttgtattatatat-ttttatctattctcgttcaagccatattctcatattataagctgaactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT
upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| ||| | || | | |||| || | | || | | | | |||| || || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || | || || ||| |||||||| ||| || |
catttggtagttgtattatatat-ttttatctattcttgttcaagccatattctcatattataagctgtactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT
upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 3
--gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| | ||| | || | | |||| || || || | | || | |||| || || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| || || |||||||| | || || ||| |||||||| ||| || |
taatttggtatttgtattatat--aatttatttattatcatgcaagccatattcttatgttataagctgtactcacctgttgcactcgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATATACAAGCACGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
gtataac putative branch site (score: 3)
tgttctttctt putative PPT
tataacataaaaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - -gtctgtt
- - - - - - - -catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa