Sequence
atgc intronic sequence ATGC exonic sequencegttacaagtttgaactttcaactcaaacgcgattgcgtttatttgttgattgagtgccgtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
Basic information
species | Glycine max |
transcript | GLYMA06G18170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------gttacaagtttgaactttcaactcaaacgcgattgcgtttattt-gttgattgagtgccgtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
| || | | | | | | | ||| | || | | | |||||| | | || | || || | | ||| |||| | |||| ||||||| || || ||||| ||||| | || || ||||| ||||| || ||||| ||||| || |||||||||||||||||||| || |||||||| |||
gtgggagacatatccttcacgatttcactgctggttgaatgagatatgttcatctagtgttctttttgcctctattctgcttctagaggtttttgagtactgaaata-gtatttcttttcctcgccacaatct--atttctgcagACCTTTGTTTATGGTGATCTTTATCGCTACGATGTAGAGAAAAATGAGTGGAAGTTGGTATCTAGTCCTAACAGTCCTCCTCCACGAAGTGCTCACCAAA
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g40740.2 (Oryza sativa), 3'ss of exon 3
------------------------------------------gttacaagtttgaactttcaactcaaacgcgattgcgtttattt-gttgattgagtgccgtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG---------------------------------
| || | | | | | | | ||| | || | | | |||||| | | || | || || | | ||| |||| | |||| ||||||| || || ||||| ||||| | || || ||||| ||||| || ||||| ||||| || |||||||||||||||||||| || |||||||| |||
gtgggagacatatccttcacgatttcactgctggttgaatgagatatgttcatctagtgttctttttgcctctattctgcttctagaggtttttgagtactgaaata-gtatttcttttcctcgccacaatct--atttctgcagacctttgtttatggtgatctttatcgctacgatgtagAGAAAAATGAGTGGAAGTTGGTATCTAGTCCTAACAGTCCTCCTCCACGAAGTGCTCACCAAACAGTTGCCTGGAAGAATAATATATACATGTTTG
upper sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 3
gtta--caagtttgaactttcaactcaaacgcgattgcgtttatttgttgattgagtgcc--gtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
|||| | | |||| || | | ||| ||| |||||| | ||||| | || | || | | | | | ||||||||| || ||||| ||||||| ||| |||||||| ||||||| ||| ||||| || ||||| || || || ||||| ||||||||||| |||||||||
gttagctttgcacaatcttttttcttcagagtt-ttgattttctttgttaag-gagtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgagtgccgtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
tgttgat putative branch site (score: 4)
aatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacaagtttgaactttcaactcaaacgcgattgcgtttatttgttgattgagtgccgtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC