Sequence
atgc intronic sequence ATGC exonic sequencegttctaagctaaaactctttcatcaggtgcttcctttttccatcagcaactaacttgagtagatgttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48520.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G05190.2 (Glycine max), 3'ss of exon 3
--------------------------------------------gttctaagctaaaactctttcatcaggtgcttccttt-----ttccatcagcaactaacttgagtagat--gttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
|| |||| | | || ||| | | || || || || |||||| || | ||| ||| |||| | |||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||| ||| |||||| | |||||||||||||||
gctagtgctatattatggtcttgtacttttctttctagtctagtgtagcaagcgctagattgtttttcatttttctttcttcagacttgtattcttaaataacttctgttattctgtttagAGAACAATTACAATGAGGAAAAAGGAAGGGCTTGCTGATTATCGATATTTTCCAGAACCAGACCTTCCAGCAGTAATCCTTTCTCAAGAATATGTTGATG
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G34500.1 (Glycine max), 3'ss of exon 3
--------------------------------gttctaagctaaaactctttcatca-----ggtgcttcctttttccatcagcaactaacttgagtaga--tgttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
|| ||| || | || ||| | |||| || || || |||||| || |||| ||| |||| | |||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||| ||| |||||| | |||||||||||||||
gtgtaatcttgtacttttctttctagtctagtgtagcaagtacaagattgtttttcatttttatttcttcagacttgtattcttaaataacttctgttattctgtttagAGAACAATTACAATGAGGAAAAAGGAAGGGCTTGCTGATTATCGATATTTTCCAGAACCAGACCTTCCAGCAGTAATCCTTTCTCAAGAATATGTTGATG
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26002 (Selaginella moellendorffii), 3'ss of exon 3
-----------------gttctaagctaaaactctttcat-caggtgcttcctttttccatcagc--aactaacttgagtagatgttc-----agAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
|| | | || || || || |||| | | | | |||| | | || ||| ||| || || ||| | ||||| || ||||| |||||||||||||||||||| |||||||||| || || | | | || || | |||||
gtgcaagagactagactgtgggaggaaggaagtcaggcacattggcacttctggtctttgacgatcgagctaattgagattttcgtgtgtgatagAGAACTGTCACTATGCGTGCGAAGGAGGGTCTTGCAGATTACCGCTACTTTCCAGAGCCAGATCTTCTCGAGCTTGTATTGAAGCAGGAGCAAGTTGACT
upper sequence: AT1G48520.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14409 (Selaginella moellendorffii), 3'ss of exon 3
gttctaagctaaaactctttcatcaggtgcttcctttttccatcagcaactaacttgagtagatgttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
| | | | || ||| ||| || | | | || || || | ||| ||| || || ||| | ||||| || ||||| |||||||||||||||||||| |||||||||| || || | | | || || | |||||
---------gtacattggcacttctggt-ctttgacgatcgagctaattgagattttcgtgtgtgat-agAGAACTGTCACTATGCGTGCGAAGGAGGGTCTTGCAGATTACCGCTACTTTCCAGAGCCAGATCTTCTCGAGCTTGTATTGAAGCAGGAGCAAGTTGACTMapped 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|125081469|gb|EL142680.1|EL142680EST: AAGCAGACCAGATTGTAACGGAGACTCGGCTATGGGAAGAAGGCGCTCAG AAAACAGTAACAATGAAGGAAAAAGGAAGG
genomic: AAGCAGACCAGATTGTAACGGAGACTCGGCTATGGGAAGAAGGCGCTCAGgttctaagct ... agatgttcagAAAACAGTAACAATGA-GGAAAAAGGAAGG
EST:
gi|164204491|gb|ES031824.1|ES031824EST: AAGCAGACCAGATTGTAACGGAGACTCGGCTATGGGAAGAAGGCGCTCAG AAA-CAGTAACAA
genomic: AAGCAGACCAGATTGTAACGGAGACTCGGCTATGGGAAGAAGGCGCTCAGgttctaagct ... agatgttcagAAAACAGTAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttcatcaggtgcttcctttttccatcagcaactaacttgagtagatgttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
aactaac putative branch site (score: 1)
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctaagctaaaactctttcatcaggtgcttcctttttccatcagcaactaacttgagtagatgttcagAAAACAGTAACAATGAGGAAAAAGGAAGGGCTTGCTGATTACCGCTACTTTCCAGAACCAGATCTTCCAGAAGTTATCCTTACCCAAGAATATGTTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT