Sequence
atgc intronic sequence ATGC exonic sequence...tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
-tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtt--tctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
| | | ||| ||||| | |||| | | | || | ||| || | | | ||| ||| | || || | |||||||| || || | ||||||||||| || ||||||||||||||||||| ||||||||| |||||
cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttc---ttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
----tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
| || || | || || | | || |||| |||| || ||| || | | | ||| ||| | || || | |||||||| || || | ||||||||||| | ||||||||||||||||||| ||||||||| |||||
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatt-tgccctctttttcctttctttcctttttcacttc---ttcattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
--tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgtt--gcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
|| | |||||||| | | || |||| | ||| | | | | | | |||| ||| |||| ||||||| || |||||| ||||| ||||||||||||| || ||||||||||||||| ||| ||| ||||| |||||
cttgatgtgggtagatgat----ttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttttttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTMapped 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|125144645|gb|EL180203.1|EL180203EST: TGTTATGGCTCCTCCTCAG ATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACT
genomic: TGTTATGGCTCCTCCTCAGgttttttttt ... tttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACT
EST:
gi|124980046|gb|EL053028.1|EL053028EST: TGCAACAACATCCTTCTCTTTATCATCCTGGTGTTATGGCTCCTCCTCAG ATGGAGCCTTTACCAAG
genomic: TGCAACAACATCCTTCTCTTTATCATCCTGGTGTTATGGCTCCTCCTCAGgttttttttt ... tttgttgcagATGGAGCCTTTACCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
tcttaat putative branch site (score: 3)
tttttgtt putative PPT
ttaatgttttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtttctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - agaaaag
- - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg