Sequence
atgc intronic sequence ATGC exonic sequencegtaaggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50500.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------gtaa---ggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttt-tccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
||| || | ||| ||| | | || | | || | ||| | | | | |||| | | ||||| || || |||| | | | | | | ||| |||||||||| |||||||||||||| || || || || |||||||||||||| ||||| ||||||||||| | || ||| | ||| | || || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggac-aatgctattatcatgcgg--aactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgccgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA
upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------gtaaggccatgagacc--aattcctctgtctagagttcaaaccagctt---atccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtg----ttacatttttc------cagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
|||| | |||| || | | | |||| ||| | | | ||| | | || || || | | | | ||| | || | ||| ||| |||| ||||| ||||| |||||||| || || || || |||||||| ||||| || |||||||||||||| | || ||| | ||| | || || |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCAMapped 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|124768642|gb|EH858772.1|EH858772EST: ATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG CTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGG
genomic: ATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccat ... atttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGG
EST:
gi|124912723|gb|EH986714.1|EH986714EST: CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG CTTGCAGATGTATGGTCTTGCGGTGTAACATTA
genomic: CTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccat ... atttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
catttttcc CT-rich tract
aaatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccagCTTGCAGATGTATGGTCTTGCGGTGTAACATTATATGTAATGTTGGTTGGAGCTTATCCATTCGAGGATCCACAGGAGCCACGAGATTATCGAAAGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT