Sequence
atgc intronic sequence ATGC exonic sequenceGCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat...
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05420.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaac---tctccccctacctctatttgttatcaatttttgtttgtcaattagt--ccccttttgaattgcagctgttgatttgggtttagggttttcaat
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GCGTGTGGAACTACGTCGTGACGGCGCACAAGCCCACCAGCGTCACCCACTCCTGCGTCGGCAACTTCACCGGCCCCAACCAGCTCAACCTCATCGTCGCgtccgtaatctattccccccttcctcccccctctcgccctccaaatctagggttttgctgcgtcactcccactcccgcctccccctcggggtcgggatcg-----
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA05G30530.1 (Glycine max), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactct--ccccctacctctattt--gttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat
| |||||||||||| || || ||||||||||| |||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||| ||||||| | || ||| | | | | | | | ||| || || | | |||||| | | || | || | | || | || | ||| || ||
GTATATGGAACTACGTCGTCACAGCTCACAAACCCACCAACGTCACTCACTCCTGCGTCGGCAATTTCACCAGTCCTCAAGACCTCAATCTCATTATCGCgtatctactcctattccctttcgttttcctagggtttcatttcttctctttcaatttcgtcaccgtttatttac--cctttcacttcgtttttt--cttccag-
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgta-cgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat
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CTATATGGAACTACGTCGTCACGGCTCACAAGCCCACCAACGTCACCCACTCCTGCGTCGGCAATTTCACCAGTCCTCAAGACCTCAATCTCATCATCGCgtatctactcattctctttccttttcctagggttcctttcttctctttcattttcatctccacttatttac--cctttcacttcgttttt---cttccag-
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat-
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GCGTGTGGAATTATGTTGTTACGGCTCACAAGCCCACCAATGTTACGCACTCCTGCGTCGGCAATTTCACTGGCCCTCAGGAGCTCAACCTCATCATTGCgtatgta-ttgcatttttctttctattctttctctttgtgtgtgaatgtgttaggtttctctttgttggccattctcatgccaagaaaaatgctagggttt
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ30457 (Selaginella moellendorffii), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat
|| ||||||||||| || || || ||||| ||||||| ||| || |||||||||||||| || ||||| || || || |||||||||||||| |||||| || || | || ||| ||| | | | | ||||| | | ||| |
GCGTCTGGAACTACGTCGTCACTGCGCACAAGCCGACCAATGTGACGCACTCGTGCGTTGGAAATTTCACGAGCCCCCACGAGCTCAATCTCATCATCGCgt----aagtccctgtttagctcctcttgcgctt--ctcctctcactcaatca-tttcctccag------------------------------------
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 1
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat
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GCGTCTGGAATTACGTCGTCACTGCGCACAAGCCAACCAATGTGACGCACTCGTGCGTTGGAAATTTCACGAGCCCCCACGAGCTCAATCTCATCATCGCgt----aagtccctgtttagctcctcttgcgctt--ctcctctcactcaatca-tttcctccag------------------------------------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|116483004|gb|EG525596.1|EG525596EST: TCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGC GAAATGTACTCGAATCGAGATCCATTCGCTTACCCCACAAGGACTTCAG
genomic: TCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaact ... ctgttctcagGAAATGTACTCGAATCGAGATCCATTTGCTTACCCCACAAGGACTTCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTCATGGAACTACGTTGTTACGGCTCACAAACCGACCAGTGTCACTCACTCGTGCGTTGGCAACTTCACAAGTCCTCAAGAGCTCAATCTCATTGTCGCgtacgaaactctccccctacctctatttgttatcaatttttgtttgtcaattagtccccttttgaattgcagctgttgatttgggtttagggttttcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccccttt