Sequence
atgc intronic sequence ATGC exonic sequenceATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G43190.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g64770.2 (Oryza sativa), 5'ss of exon 6
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttctt-ttctctctctctctctctcttctattc-gttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
|| ||||| ||||| || || || || |||| || || |||||||| |||||||||||||||||||| |||||| | ||||| || || ||||| || |||||| |||| | ||| ||||| |||| | | || || | || || | | | | || || || | | || | || | |
ATTCATCATATGCTTTACCCTATAACCATTGAAGTGCTTCATCAAGTGTTTTCTCCCTATGGATTTGTGGAGAAGATAGTCACATTTCAAAAGTCAGCCGgtcagattctttctacctctcattctcactctattcttgcatttaatgcagtgttttccttgccagatagcatgcagattatgaggcgtatttcatagtt-------------------------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G08870.1 (Glycine max), 5'ss of exon 6
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttcta----ttcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
| ||||||||||||||||| || || | || || || |||||||| ||||||||| |||||||||| || ||| | || || ||||||||||| ||||||||| ||||| || || |||||||| ||| | || || || |||| | | | | || | || || ||||
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTCCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagattttttttttgtcttaggggccttcacggggtgaattgaggatatatt--tggt-------------------------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G27970.1 (Glycine max), 5'ss of exon 4
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttcta----ttcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
| ||||||||||||||||| || || | || || || |||||||| ||||||||| |||||||||| || ||| | || || || |||||||| ||||||||| ||||| || || |||||||| ||| | || || || |||| |||| | || || | || || ||||
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagatttttttttgttttagggggccataatggggtgaattgaggatatatt--tggt-------------------------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
| ||||||||||||||||| || || || || || ||| ||||||| ||||||||| |||||| ||| || ||| | || || || |||||||| ||||||||| ||||| || | |||| || ||||| ||| || | | ||| | |||| ||| | || | | | | || | | ||||| |||
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctc------tcagatttctccctttctcttctttccatccctattaac----------atttttgtgttcctagacttta----actaggtagcttgaggttatatttttgt---------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 5'ss of exon 5
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctct---tctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
|| |||||| |||| || || || || || || || ||||||||||| |||||||| |||| ||||| |||||| | ||||| || |||||||| |||||||||||||| | ||| | ||| | ||||||| || ||| | | ||| | | | || || | | | | | | ||||
ATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGATTGTCACGTTTCAGAAGTCAGCTGgtcagcttcttcaagttttctctctttatctctcttgtgctgtctctctatctcttaattcttaattctcctttcaactct-tgaggactagctggatggt-------------------------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S36_37V6.1 (Physcomitrella patens), 5'ss of exon 4
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
|| || || ||| ||||| || || || || || ||||| ||||| ||||| ||| |||| |||||||||||| ||||||| ||| ||||| ||||||||||||||| |||| | | || ||||||| ||||| ||| | || ||| | ||| ||| |||| | | ||| || |
ATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCCCATGGCTTTGTCGAGAAGATCGTCACCTTCACAAAGTCAGCTGgtcagcttctc-----ttctgtcttggctatctctctgccttctgcctttttcgggccc---ttttctttcaccatttttctctttctggcgggtagtca----aaggtggg-----------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S48_128V6.1 (Physcomitrella patens), 5'ss of exon 6
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
|| || || ||| ||||| || || || || || ||||| ||||| ||||| || |||| |||||||||||| ||||||| ||| ||||| ||||||||||||||| |||| | | || ||| |||||||||| || | | || ||| | ||| ||| |||| ||| ||| |
ATACACAACCCGCTCTATCCTATCACCGTGGATGTGCTGCACCAAGTGTTTTCCCCTCATGGCTTTGTCGAGAAGATCGTCACCTTCACAAAGTCAGCTGgtcagcttctc-----ttctgtcttgactatctatctctcttctggcttttgtgggcccttttttt-tttcaccatttttctctttc-tgtcgaaggtgaacacagg----------------------------------------------------------------------------------
upper sequence: AT1G43190.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ25472 (Selaginella moellendorffii), 5'ss of exon 5
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattc-gttt--tagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
|| || ||| ||| ||||| || || || || || ||||||||||||||| || |||| |||||||||| ||||||| ||||||||||| |||||| |||| ||| | || || || | | | ||||| |||||||| || | ||| | || ||| | |||| | | || || | |||| | | | |||| || | |
ATTCACCACCCGCTCTATCCCATCACCGTGGATGTGCTGCATCAAGTTTTTAACCCTCATGGCCATGTCGAGAAGATCGTCACGTTCCAGAAGTCAGCTGgttagctcctctcgtctactcttaactttttatttctcttttctattctgtctcgtaggctttgctgttgcttgtgattttgcgaagctacttttctttttgccttttat-cattcgtgcttttgacgcag-------------------------------------------------------------Mapped 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|163993811|gb|EL999334.1|EL999334EST: TCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTG GTTTTCAAGCTCTTATACAGTATCAGGTACAACAGTGTGCTGCCTCTGC
genomic: TCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttct ... gactatttagGTTTTCAAGCTCTTATACAGTATCAGGTACAACAGTGTGCTGCCTCTGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGCTCGTCACTTTCCAGAAGTCTGCTGgtcagcttctccgcatttcttttctctctctctctctctcttctattcgttttagcttagagaattatttgaaagtttgtctgtttcatgttattggtctctttaaaataatattgctgttaaaactttgtatttgccatctaacagtttgatgattgttaactataagcttgtttgttgactatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT