Sequence
atgc intronic sequence ATGC exonic sequencegttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 6
gttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
||| || ||||||| | | | || | || ||| || | | || ||| || ||||| ||| ||||||| | |||||| | || || | || || |||||||| ||||||||||||||| | || || |||||||| ||||| ||||| || |
-------------------------gtcactgttgc-ccatcatttc-ttatctagtagattatctcatctgtctttttgtttatggagatttttttttctc----tgcagGGCACCATTGCTGAAGGTGCTCCAGTGGTGCCAATATCTGCTCAACTGAAGTACAACATTGATGTGATCTGTGAATACATTGTGAAGAAAATCCCCATTC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
gttaggttttcttat-ctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
|| | | | | | || || | | | || ||| || |||| | || || || |||||| | || || | ||| | ||||| | ||||| | ||| || | || ||| | || || || |||||||||||||||||||| | ||||| |||||||| ||||| ||||| ||||
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagt---gtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATA--GCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 6
gttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
|| || |||| |||| | ||| | || || | | ||| | || ||| || | | || | | || ||| | | ||| ||||||||||||| ||| || | || ||| | |||||||| |||| || || |||||||| ||||| ||||| ||||| ||||||||||||||||
gtaagttttttttataa---agagatttcttttacacaagtgaattcctt--ttcaataacttacatgat----aattctccccc----ctttttttgtgacttac--cagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGTGAGTATATTGTGAAGAAGATCCCAATCC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
gttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
|| |||||||| | ||| | || || | | ||| | || | ||| ||| | | || || | | ||| || ||| ||||||||||||| ||| || | || ||| | |||||||| |||| || || |||||||| |||||||| || ||||| ||||||||||||||||
-gtaagttttctt----taaagagatttcttctacacaagtgaattcctt--tttgataacttaaatg----acaatttcccccc------ttttttgtgatttgc--cagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
ttctaaa putative branch site (score: 2)
tttctttcacatcct CT-rich tract
ttctaaaatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggttttcttatctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG