Sequence
atgc intronic sequence ATGC exonic sequencegtaattcatcatctgattctgattttagggtttgtacgagtgtttttccggtggttaactagcgttttccggtgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCAGTGAATACTCAATGGAAGCTTACAAGAAATATGGAGTTCTTAAAGGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g15970.5 (Oryza sativa), 3'ss of exon 2
--------------------gta-attcatcatctgattctgattttagggtttgtacgagtgtttttccggtggttaactagcgttttccggtgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCAGTGAATACTCAATGGAAGCTTACAAGAAATATGGAGTTCTTAAAGGCAC
|| | ||||| | | | | ||| | | | | | || || || | || || ||||||| ||||| || | |||| |||||||||||| || || ||||||||||| ||||| ||| |||| ||||| ||||| || ||| || || ||
tcttaaacccttgtatttatgtgcagcaatcattggccttgcgcccttgccttttgatatcaactatatctcta--tagcttgctctcctttatgtgaa-cagGAGAAATATCACCCTTACTACCCTCAAGCTGCCGTTATGTGCCAACTTGCAGTGAGTACTCTATGCAAGCATACAAAAAATACGGTGTTGCAAAGGGTAC
upper sequence: AT3G09310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g15970.4 (Oryza sativa), 3'ss of exon 3
--------------------------------------------gta-attcatcatctgattctgattttagggtttgtacgagtgtttttccggtggttaactagcgttttccggtgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCAGTGAATACTCAATGGAAGCTTACAAGAAATATGGAGTTCTTAAAGGCAC
|| | ||||| | | | | ||| | | | | | || || || | || || ||||||| ||||| || | |||| |||||||||||| || || ||||||||||| ||||| ||| |||| ||||| ||||| || ||| || || ||
gtgagttcattcttgctgttttcatcttaaacccttgtatttatgtgcagcaatcattggccttgcgcccttgccttttgatatcaactatatctcta--tagcttgctctcctttatgtgaa-cagGAGAAATATCACCCTTACTACCCTCAAGCTGCCGTTATGTGCCAACTTGCAGTGAGTACTCTATGCAAGCATACAAAAAATACGGTGTTGCAAAGGGTACMapped 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|86075728|gb|DR371485.1|DR371485EST: GGAGAGTGTGGGAGTCAAAGCAGCTTTAGCAATGCTGAGATTCTACAAGA GAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCA
genomic: GGAGAGTGTGGGAGTCAAAGCAGCTTTAGCAATGCTGAGATTCTACAAGAgtaattcatc ... tgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggtttgtacgagtgtttttccggtggttaactagcgttttccggtgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCAGTGAATACTCAATGGAAGCTTACAAGAAATATGGAGTTCTTAAAGGCAC
ggttaac putative branch site (score: 3)
tgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcatcatctgattctgattttagggtttgtacgagtgtttttccggtggttaactagcgttttccggtgaaaaacagGAGAGATATCGCCGGTGTTACCTAGAAGCTGCCGTTACGTTCCGACTTGCAGTGAATACTCAATGGAAGCTTACAAGAAATATGGAGTTCTTAAAGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA