Sequence
atgc intronic sequence ATGC exonic sequenceTTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05470.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 2
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
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AGTTAAGAATATAAGGAGGAGGATGACACCACAGCCACTTAAGATCCGTGCTGATGTTGAGATGAAATGTTTCCAATTTGATGGGGTGCTTCACATTAAGgttcttgttatcc----------ctgtgtcttcccttagggtttactgaaacttttt--cttatggctaattctggttggtt-ttgcag-----------
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G058138_T01 (Zea mays), 5'ss of exon 2
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
||||| |||| |||||||| |||||||| |||||| | ||||| ||||||||||| || ||||||| || |||||||||||||| ||||| || ||||| || || | || | || | | ||| | | | || ||| || || || | ||
GGTGAAGAACATAAGGAGGAGGATGACACCGCAGCCACTCAAGATCCGTGCTGATATAGAGATGAAGTGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttggccctgttggtgtccttgtgatttgacaatggtatttgcaaaaa--ctaattgtatctgtatttgcag----------------------
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 2
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
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GGTTAAGAACATAAGGAGGAGGATGACACCACAGCCTCTCAAGATCCGTGCTGATATAGAGATGAAATGCTTCCAGTTTGATGGAGTGCTCCATATTAAGgttctagttgcccctaatgccacccttgtgatttaacaatggtatttgcaaaaaa-ctaattgta--tatgtatttgcag--------------------
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G35600.1 (Glycine max), 5'ss of exon 4
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgttt---gttttctacttctagctaaagatgtt--tggctattattatgaatttacag----------------------------------
| ||||| | ||||| || ||||||| || || || |||| ||| | || ||||||||| |||| |||||||| |||||||||||||| ||||| |||||| || | | ||| | |||||| || |||| | || | | ||| | | | || | | |||| | |||| | | | ||
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtcttgattatttctattcct-cctgtttcttattttggcttcttttcttttaagcatctaatttgttatgtgaagtgttatttcctatagcttatcttccaaagtattctcacgttttataatgatttgattatgcag
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 4
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgtt--ttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag-------------------------------------
| ||||| | ||||| || ||||||| || || || |||| ||| | || ||||||||| |||| |||||||| |||||||||||||| ||||| ||||| | || | | | | |||||||| ||| ||| || ||| || |||| || || || ||| ||| || | |
TGTGAAGAATATTAGAAGACGAATGACCCCCCAACCCTTGAAAATTAGGGCAGATATTGAAATGAAATGTTTTCAATTTGATGGAGTTCTTCACATTAAGgtatttgattatttgtattccttttgttttttactttggttccttttcttttaagcatctaatttgttatatgaatttttattgcctatagcttatcttccaaagtattctcaggttttataatgatttgattatgcag
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g07100.t01 (Vitis vinifera), 5'ss of exon 4
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttt--tcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
| ||| ||||||| ||| ||||||||||||| ||| | || || |||||||| || ||| |||| ||||| ||||||||||| ||||| ||||||||||| || | ||| | || || ||| | ||||| | ||| | | | | |||||| | | | || | | |
GATCAAGAACATTAGAAGGCGAATGACACCACAACCATTAAAAATCCGTGCTGACATAGAAATGAAATGTTTCCAGTTTGATGGTGTTCTTCACATCAAGgtattgattgttcttccggtaccattatttctttatctttgtaagttttgtggaagatggggcacaaccatgctgtgtttgcatgagactgtg--tcaatgg
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 4
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtc--agtcttttcctttttcttatctgttttttttttttgttttctctg-tttgttttctactt-----ctagctaaagatgtttggctattattatgaatttacag-------------------------
| ||| | |||||||| |||||||| ||||| ||| |||| ||||| |||||||||||| |||| ||||| ||||||||||| ||||| ||||| ||||| | | | ||||| || || ||| |||| |||| || || | ||||| || || | || ||| | | || | | || |
GGTAAAGAATATTAGGAGAAGAATGACTCCACAACCATTGAAAATTCGGGCTGATATTGAAATGAAATGTTTCCAGTTTGATGGTGTTCTTCACATTAAGgttttattggtgtccttctttgccactttttattttatttgattggcctaatctgtttcataattgggattttactttagaaccgttttaagtactgtctgctttaatacttgttttatctttcactattcag
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 5
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcc---tttttcttatctgttttttttttttgttttctctgtttgttttctact-tctagctaaagatgtttggctattattatgaatttacag
| | | | |||| | ||||| ||||| || |||||| |||||||||||||||||||||| ||||| || |||||||| ||||| ||||| ||||||||||| || || | | || || ||||| ||||| |||||| ||| | | || | | | | | | ||| | | | | ||||
TATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagttacagctgttactcgagcatttttatttttatttttcttggttcatgctgtaatgttttggtctacgggttagctggaaaatcagcattt----
upper sequence: AT5G05470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S352_15V6.1 (Physcomitrella patens), 5'ss of exon 5
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtc--ttttcctttttcttatctgttttttttt-tttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag-
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CATCAAGAACATCAAAAGAAGAATGACCCCTCAGCCATTGAAAATTCGTGCTGACATTGAGTTAAAATGTTTTCAGTTCGATGGGGTTTTACATATTCAGgtgagacaatgttgctattgcctaaaagttcatctgcacttgtttgtgctcagtgttgtagattgcctgt--attatagttggc-acggctat-aacgtagagaMapped 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|86075249|gb|DR371006.1|DR371006EST: CTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAG GAAGCCATGAAGAAGGCAGAGGCTGTAGGTACTGATGATTGTCCAGTCAAA
genomic: CTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttt ... gaatttacagGAAGCCATGAAGAAGGCAGAGGCTGTAGGTACTGATGATTGTCCAGTCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTGAAGGACATTAGGAGGAGAATGACACCACAGCCAATGAAGATTCGTGCTGATATTGAATTGAAGTGTTTTCAGTTTGATGGAGTTCTCCACATCAAGgtcagtcttttcctttttcttatctgttttttttttttgttttctctgtttgttttctacttctagctaaagatgtttggctattattatgaatttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA