Sequence
atgc intronic sequence ATGC exonic sequenceACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08565.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os07g43060.1 (Oryza sativa), 5'ss of exon 1
-ACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttc---ttctcttgcgaatattttttgcctaatctggtttct--ccaacag---------------
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GATGATGGACGACGGGCCCAA-GTACGCGCAGATACCGACGAGCTTCGGCCACGAGCTCCGCGCGTGCCTCCGCTGCCGCCTCGTCAAGACCTACGATCAGgtgcgcaccgcccccgagctcctcgcctcgacggcttagggtttcgtgttcatgcttgtttccgtatcgaatcgagggttaatgcttattcgggaggagt
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G086805_T02 (Zea mays), 5'ss of exon 1
ACAAATCACAATGGGAGAA-GCGCC-TGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctc-----ttgcgaatattttttgcctaatctggt--ttctccaacag------------------
| | | | ||| | ||| ||| |||| ||||| |||||||| | |||||| | || || || |||||||||||||||||||||||||| ||||| | ||| || | | | | | | ||| ||| ||| | || | | | | | | | || |
--GGACGATGAAGAGAGGGTGGGCCATGCGGAGATCCCGACCAGTTTCGGTCCCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgt----accctcctgcggcac-cgctccccttctctctcctcacgctttggggatgcggtgtaggttcaccagccgtccgttgacgggagggttataggactgtg
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA17G00250.2 (Glycine max), 5'ss of exon 2
ACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
| | ||||| | || ||||| || ||||| || || || ||||| ||| | |||||||||||||| |||||||| ||||| ||||| |||||||||| | | || | | | | ||| | | || || | ||| | | ||| || | | | ||
CTTACAAAAAATGGCAACTGCACCTGCACAAATTCCTACAAGCTTTGGCCATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtaccctactaccctttatttttcatcattgtttt-ttgtttacaatttctgtttttgtttcacagttcag---
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA17G00250.1 (Glycine max), 5'ss of exon 2
ACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
| | ||||| | || ||||| || ||||| || || || ||||| ||| | |||||||||||||| |||||||| ||||| ||||| |||||||||| | | || | | | | ||| | | || || | ||| | | ||| || | | ||||| |
CTTACAAAAAATGGCAACTGCACCTGCACAAATTCCTACAAGCTTTGGCCATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtaccctactaccctttatttttcatcattgtttt-ttgtttacaatttctgttt----ttgtttcacag----
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv10s0071g01040.t01 (Vitis vinifera), 5'ss of exon 1
-ACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgt---------gatttgcgtgtttcttctcttgcga-------atattttttgcctaatctggtttctccaacag-------
| | | | ||| | |||| |||||||||||||| || ||||| |||||||| || ||||| || || ||| | |||||||| |||||||||||||||| | | | ||| || | | ||| | | | | ||||| | || | ||||| |
GAGAGAGAGAGAGATGAGCAACGCC-GCCCAGATTCCGACCAGCTTCGGGCACGAGCTCAGAGCTTGCCTCCGTTGCAGGCTCGTCAAAACCTACGATCAGgtctttcctttttctctgtttggtttctcagagagtaaagcccttcctttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcag
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ10606 (Selaginella moellendorffii), 5'ss of exon 1
ACAAATCACAATGGGAGAAGCGC-CTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
| | | | | | | | | |||||| | || |||| || ||| || || | |||||||||||||||||||| ||||| |||||||||||||| | | || | | | | || | | ||| || ||
--ATGGGAGGAGGACACCATCACGCCGCCCAGGTCCCCGCGAGCTTGGGCAGGGATCTACGCGCTTGTCTTCGATGCCGCCTTGTCAAAACCTACGATCAGgtg-agctcacgccgtggttcttagagcgatcgattgattttcattcccgattcttcgcag-------------------
upper sequence: AT5G08565.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ35348 (Selaginella moellendorffii), 5'ss of exon 1
ACAAATCACAATGGGAGAAGCGC-CTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctgg--attctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
| | | | | | | | | |||||| | || |||| || || || || | |||||||||||||||||||| ||||| |||||||||||||| | | | | || ||| || | ||| || | || ||
--ATGGGAGGAGGACACCATCACGCCGCCCAGGTCCCCGCGAGCTTGGGGAGGGATCTACGCGCTTGTCTTCGATGCCGCCTTGTCAAAACCTACGATCAGgtgagctcacgccgtggtttcttagagcgatcggttgatttccattcccgattcttcgcag---------------------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|164160751|gb|ES029470.1|ES029470EST: GCCGCCTCGTCAAGACCTACGATCAG TTTAGGGATTCTGGATGCGAGAACTGTCCTTTCTTCAAAATAGAAGACGAT
genomic: GCCGCCTCGTCAAGACCTACGATCAGgtctggattc ... tctccaacagTTTAGGGATTCTGGATGCGAGAACTGTCCTTTCTTCAAAATAGAAGACGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACAAATCACAATGGGAGAAGCGCCTGCCCAGATTCCGACGAGTTTCGGCCACGAGCTTAGGGCTTGTCTTCGATGCCGCCTCGTCAAGACCTACGATCAGgtctggattctcttgtcacttgtgatttgcgtgtttcttctcttgcgaatattttttgcctaatctggtttctccaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT