Sequence
atgc intronic sequence ATGC exonic sequence...atttgttctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33845.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g15520.1 (Oryza sativa), 3'ss of exon 1
atttgttctgctctggtactcaattggtgattcatagt--gggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
|| || || | | | | | | || | | | | | || ||| | | | | | | ||| || |||| || | ||||||||| || ||| |||||| ||| | | | |||||||| | || |||||||||||||| ||||||||||||||||| || || ||||| || |
tttcgtgct--tttaaattttagtcactaatctctctttcgagatatgaagttttgaagtgcttgagctcatttttttgtgcttttggttctacttttgcagTGGACATGCTGATGCCAGGAAATACAGCAATCTTGCGGAATGCGAGAATCGATATGTTCAAGGGCTCAATGAGGCTTGCTGTCGACAAGTGGGGACGTGT
upper sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G825437_T04 (Zea mays), 3'ss of exon 1
----atttgtt-ctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
|| | |||| | | |||| | | ||| | || | | || |||||| | | |||| | | | ||| | |||||| || ||| |||| || | || || |||| | || ||||| || || || |||||||| ||||||||||||||||| || || |||||||| || ||
ttgttttcatggttgctatcatgttcaactaattgttctgactgtg--attttttcttttggata--actttcagtccgtgtgatgtgctatcctcctt-tgcagTTGATTTGCTGAAGCCCGATGCCACGGTGATCTTGCGCAATGCCAAAATCGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAATGGGGGCGGAT
upper sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G067522_T01 (Zea mays), 3'ss of exon 1
--atttgttctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
|| || | ||| | || | |||| || | | | | | || | | | | | ||| || | | | |||||| || ||| |||| || || || |||| | || ||||| || ||||| |||||||| ||||||||||||||||| || || || ||||| || ||
tggcttctttttatctttgatgtcatgtggacgtcatggttgatgattgttttgactgtgcatttgtcctgggcttatgatgtgctcttctcctt--tgcagTTGACTTGCTGAAGCCCAATGCGACAGTGATCTTGCGCAATGCCAAAATAGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAGTGGGGGCGGAT
upper sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G37050.1 (Glycine max), 3'ss of exon 1
atttgttctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctt-tcttggt-----ttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
|||| | | | | | || | | || | | | ||| || | | | || || | |||| || ||| | |||||||||| ||||| | || || ||||| | ||| || ||||||||||| || |||||||||||||| ||||||||||| |||||||||||||| || ||
------tctgtttggtgaataattttgaagtgtttaattttgaattagatgtttcattggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
upper sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G33380.1 (Glycine max), 3'ss of exon 1
atttgttctgctc-tggtactcaattggt-gattcatagtgggtcacttagctttttgggggcta-atacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
| | | | | | | || |||| ||| | | | || | || | | ||| | | | || | | || ||||||||| ||||| | || || ||||| | ||| || ||||||||||| || |||||||||||||| ||||| ||||| || ||||||||||| || ||
-tcagattggtgaataattttgaagtggttaattttgaattagatgtttcattggttcacttttgtgttatagtggtgaataactcttttactttg--tgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86079117|gb|DR374874.1|DR374874EST: TGTTGGAGATGAGACTGCTTGCATCCTCTTCACTGCTCGCAACGATCAAG TGGAATTGATGAAWCCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAG
genomic: TGTTGGAGATGAGACTGCTTGCATCCTCTTCACTGCTCGCAACGATCAAGgtgagataat ... gtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAG
EST:
gi|125048668|gb|EL120937.1|EL120937EST: CTTGCATCCTCTTCACTGCTCGCAACGATCAAG TGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAG
genomic: CTTGCATCCTCTTCACTGCTCGCAACGATCAAGgtgagataat ... gtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
ggctaat putative branch site (score: 3)
tttttattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgttctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -ctgctct
- - - - - - - - -actcaat
- - - - - - - - - - - - - - - - - - - - - - - - - tttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatacaa