Sequence
atgc intronic sequence ATGC exonic sequencegttttatcaatttctctcctctaagcaaaccctctgcatactatatctagtcacctttctaattatgttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G02100.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------gttttatcaatttctctcctctaagcaaaccctctgcatactatatctagtcaccttt-----ctaattatgt-tacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
|| | || | || || ||| || || | | | | | || | | || | ||| | |||| ||| ||||| | || ||| || |||||||| ||||| ||||||||||| | ||||||||||| ||| ||||||| | || ||
gtaggtgtttctatgtcacccgcttctctttgctctccgaactttcatctgaaactggaagagaaatgtggtccatgaaaacattggtccaggagctttggataa-ttcttgacatccttcatgttgataagaatggaggttggttgtttacgtttgcgcagATTTGGAGGGTAGCTGATGTCCCGAAGGGTGACAAATACCAGTACACGCATTTTGCTCATACTATCAATAGTTTCGACTCTGCCCCACCTACACTTCTCG
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
gttttatcaatttctctcctctaagcaaaccctctgcatacta--tatctagtcacctttctaattat-gttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
| | | || | | | ||| ||| | |||| | | || | | |||||||||| || || || | ||| ||||||||||| | ||| ||||| ||||||||||||||||| || || || ||||| || || || ||||||
------------------------gtgggcgatatggagaatcgttatatagggatctttgacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 8
gttttatcaatttctctcctctaagcaaaccctctgcatacta--tatctagtcacctttctaattat-gttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
| | | | || | | | ||| ||| | |||| | | || | | |||||||||| || || || | ||| ||||||||||| | ||| ||||| ||||||||||||||||| || || || ||||| || || || ||||||
------------------------gtgagcgatatggagaatcgttatatagggatcttttacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTCMapped 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|124963389|gb|EL037728.1|EL037728EST: TCTTCCAGGCACCGAACTGAAGGAG GTGTGGTAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACA
genomic: TCTTCCAGGCACCGAACTGAAGGAGgttttatcaa ... acttccacagGTGTGG-AAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaaccctctgcatactatatctagtcacctttctaattatgttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
ttctaat putative branch site (score: 2)
ttacttcc putative PPT
tttctaattatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttatcaatttctctcctctaagcaaaccctctgcatactatatctagtcacctttctaattatgttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA