Sequence
atgc intronic sequence ATGC exonic sequencegtataatttctatttggactactttgtgttgtttttgagttgcatctggatctgtatttaggttactgtttccttatctagtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G31070.1 (Glycine max), 3'ss of exon 2
gtataatttctatttggactactttgtgttgtttttgagttgcatctggatctgtatttaggttactgtttccttatcta-gtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
| || || || | || || | |||| |||| | ||| || || ||| || | || || | |||| ||| ||||||| | |||||||| || || |||| |||||| || || || || || ||||||||| | || ||||||||||||||||||||||| ||||||||
-----------gtatgtgctttcttttctt-cttcggttttgcgtctgtttttgtcttagaattttgattttgagatttttgtttttttgttctcg-attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTT
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G36500.2 (Glycine max), 3'ss of exon 1
--gtataatttctatttggactactttgtgttgtttttgagtt-gcatctggatctgtatttaggttactgtttccttatctagtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
| | ||||| || || | || ||| | || || || || | || | |||| | | ||| |||| | | || || | |||| | ||||||| | |||||||| || || |||| |||||| || || || || || ||||| ||| | || ||||||||||||||||||||||| ||||| ||
gtatgtgctttcttcttttcttattcggttttgcgtctgtttttgcttcagaattttgattttg---agattttgtttatttgtttttttgttattgat--tgttgcagTTTTGCCTACGATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCCTGCGTTTGGCATGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTCTT
upper sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0217g00030.t01 (Vitis vinifera), 3'ss of exon 2
-gtataatttctatttggactactttgtgttgtttttgagttgcatctggatctgtatttaggttactgtttccttatctagtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
| | | | ||||| || |||| | ||| || | | | |||| | | |||||| | | | ||| ||| | || ||||||| || |||| || || || ||| ||| || || || || ||||||||||| || |||||||| ||||||||||| ||||||||||||||
tttcttctgctttcttggaaaacagacgaaggtttct---ttgtttccat-tttctttttatgatcctgtttttgtgtttcaatatat---tctacttgttatgcagTTCTTCCGACTATGACAGTGCAAGAGCACAGTGGAAACGACAAATCTTGTGTGTGGCATGCAACGGACTTTGCAGATGGTGAACTTAAGGATGAGCTTTTMapped 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|164218632|gb|ES070940.1|ES070940EST: GGCAATCTAAAACTTTGAAGATCTGTGCTAATCACTTCG TTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTG
genomic: GGCAATCTAAAACTTTGAAGATCTGTGCTAATCACTTCGgtataatttc ... atttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTG
EST:
gi|124917155|gb|EH991029.1|EH991029EST: AGGCAATCTAAAACTTTGAAGATCTGTGCTAATCACTTCG TTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAA
genomic: AGGCAATCTAAAACTTTGAAGATCTGTGCTAATCACTTCGgtataatttc ... atttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAA
EST:
gi|125074490|gb|EL138410.1|EL138410EST: TCTAAAACTTTGAAGATCTGTGCTAATCACTTCG TTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTG
genomic: TCTAAAACTTTGAAGATCTGTGCTAATCACTTCGgtataatttc ... atttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtatttaggttactgtttccttatctagtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
ttctgat putative branch site (score: 3)
tatttct CT-rich tract
tgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatttctatttggactactttgtgttgtttttgagttgcatctggatctgtatttaggttactgtttccttatctagtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT