Sequence
atgc intronic sequence ATGC exonic sequence...tgtcactttttatctcgatgttatttccttcctgatctaactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
-----tgtcactttttatctcgatgttatttccttcctgatc-taactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
| | | | | | | || ||| || | | ||| ||| | |||||||| ||| | | | | | | || ||| | ||||| ||||| | |||| |||||||| || || || |||||||| || |||||||||||| | || |||||||| |||||||| | ||||||||| | |
gtgcttattgcatggt-tttatatattagttttagcataatcataaattcagccttttctgttctcatgctaatttgtt-----gtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 6
----tgtcactttttatct-cgatgttatttccttcctgatc-taactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
|| | || ||| | || || || || ||| | | | ||| | ||| | || ||| || | | | | ||| ||||| ||||| | |||| |||||||| || || || |||||||| || |||||||||||| | || |||||||| |||||||| | |||||||| | |
gtgctgctagttgcagtcttccatatt-ttagtttgagaatcatgataaaatcttttatcattcttatgttctct---tcttatggtggtg--gattgcctcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACATGTGTTTCTCGTTTTGAAAATCTACATCTTGTTG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 7
-tgtcactttttatctcgatgttatttccttcctgatctaactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgt-tctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
| | | |||| | | | || | ||||| || ||| |||| | | ||| | || | || | || ||| | | | |||| || | |||||||||| || || || || || ||||| || ||||| ||||| | |||||||||||||| |||||||| |||||||| | |
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatga--ctgaacgtgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 6
-tgtcactttttatctcgatgttatttccttcctgatctaactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgt-tctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
| | | |||| | | | || | ||||| || ||| |||| | | ||| | || | || | || ||| | | | |||| || | |||||||||| || || || || || ||||| || ||||| ||||| | |||||||||||||| |||||||| |||||||| | |
tttttaagttttgggtagtgtattcttggtacctgaactttgtgttcagtttttgttgattacattatatga--ctgaacatgtcatctgttttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACATATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
aattaat putative branch site (score: 3)
ttgttctcc putative PPT
aaattaatattggtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcactttttatctcgatgttatttccttcctgatctaactgtcgccttttcccctctaaaattgtctggatcccaaattaatattggttgttctccagGCGATTCTCAGACTTGCTGATGAAGAGGGCAACTATTTGCAAGATGCCTGGGAGCATATACTAACTTGTGTTTCCCGTTTTGAGCAACTACATCTCTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - -ctgatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaatt