Sequence
atgc intronic sequence ATGC exonic sequenceAACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49820.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || ||||| || || || ||||| |||| ||| | |||||||||||| ||||| || ||||||||||| || | |||||| || ||||||||||||||| | || || || || ||||| || ||| |||| | |||| ||| || ||| | || | |||| | | || || |
AACATCAACTCGAACTCCAATTTATAAGGCCTATGCAAGAGGAGAAAACATTGGAGATGTCACTGCTAAAGGCGAATCTGTTGGGAACATTGCAGATCTGgta--attattaatc--tgttgagctttcttgttact-aagtggcttgtcaat-------accaaggcttcctaatgctg--ctataaatgattg--ttgc-aacctactgatttct----------------------------------------------------------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctg---tttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || || |||||||| ||||| || || | ||| ||||||||||| || ||||| || ||||| |||||||| ||||||| || ||||| ||||||||| | |||| | || | || |||||||||| || | ||| || || | | | | || || || || |||| |||| | | | ||| | | | ||| || || |||| || | | || | | ||| | | |||| | |||||||
AACCTCGACCCGTACACCAATCTACAAGGCATATGCAAAAGGAGAAAATATTGGAGATGTCACTGCCAAAGGAGAAAGTGTTGGGAACATTGCTGATCTGgtaa-----tcattcatcttttgcatt--ttgtttcttgttggtctggttaccata------catgtagcttatatattctgctggcatcatttatgttaatagtatgctggctactaaa-atttgtcttattcagtactgcacttatatgaaaatttgcattcaatagttcactgatatttctgtctttttatgtgtgaag
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || ||||| || || |||||||| |||| ||||| ||||||||| || ||||| || ||||||||||| || | |||||| || ||||||||||||||| | | || ||| | | || ||| | ||| ||| | | || || || |||||| || ||| || || ||| |||| |
AACTTCAACTCGCACTCCAATCTATAAGGCCTATGCTAGAGGAGAAAATATTGGAGATGTCACTGCTAAAGGCGAATCTGTTGGGAACATTGCAGATCTGgtaaaaatcaatt----catca--tactgttacctct-aaatatttc-ttgttgcatggtggcatgccaaattaacatttcgtgaaatgtc-cttttttgttagtataa------------------------------------------------------------------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatt-tgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
|| |||||||| ||||| || || || || | ||| |||||||||||||| || || || |||||||||||||| ||||||| || ||||| ||||||||||| | |||| | ||||||||| | | | |||| ||| | | | || | ||| || | | || ||| | ||| | | || || || | | || | || | | | ||||| | | ||
CACCTCTACTCGAACACCAATTTACAAGGCGTATGCAAAAGGAGAAAACATCGGTGATGTTACTGCTAAAGGAGAAAGTGTTGGAAACATTGCTGATCTGgtatg-----tgttca----tgtttttcattgaacttggagcttttttttgctgccgccattgtgttattatcatattatgctttttcaat-----cactgccattttccccttctctgatttagttttgtaagatatcttttgatttacattttttgtttgtgaag---------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G40210.1 (Glycine max), 5'ss of exon 4
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgacccttt--ttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || ||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||||||||| |||||||| ||||||||||| |||||||| ||| | || |||| || | ||||||||| | | | | | |||| |||| ||| | | | |
AACCTCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAACATAGGGGATGTCACTGCTAAAGGAGAATGTGTTGGCAATATTGCAGACCTGgtatgtttttttaacttcccaacagttgctataatgctgccatgattttgttggaacattgcttgcaac--aatt---tttgcacttttctttgtcatccaatca------------------------------------------------------------------------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 3
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaa--aggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || ||||| ||||| || |||||||||||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||||||||| |||||||| || | |||| || | | ||||||||| | | | | || || | | | || | |||||| |||
AACATCAACTCGCACACCAATTTATAAAGCCTTTGCTAAAGGAGAAAATATAGGGGATGTCACTGCTAAAGGAGAATGTGTTGGCAATATTGCAGACCTGgtatgttttttaacttcctacagttgctataatgctgccattattttgttggaacattgttt---gcacctttctttctcgtccaatcaatcaactacat-gct-------------------------------------------------------------------------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
||| || || || ||||| || || |||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||| |||||||| ||||||||| | ||| || ||| ||||| | | | | || | || || | |||| ||| | ||| | | |||| || | || | | | | ||
AACATCAACCCGCACACCAATTTACAAAGCCTTTGCTAAAGGAGAAAACATTGGAGATGTCACTGCTAAAGGAGAATGTGTTGGCAATATTGCTGATCTGgtacg---cttgttaaac------tttcaat-ctccaaagatgatatgc-------atatatcaa--ggatatgaatacgggtttg-ggtgtctggaaagcaaaatgac-atatgacatgc------------------------------------------------------------------------------
upper sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ32878 (Selaginella moellendorffii), 5'ss of exon 6
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatga---ccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
|| || ||||| |||| || || || |||||||| |||||||||| |||||| ||||||| |||||||||||| | || || ||||| |||||||||||| | || | | | || | ||| | | | ||| | |
TACTTCGACTCGAGCACCCATATACAAGGCCTTTGCGCGTCGAGAAAACATTGGAGACATAACTGCAAAAGGAGAGTGTATCGGAAACATTGCGGATCTGgtatgagaacgagttgcaaggactggtagt--ttgctaacacgctactttttag----------------------------------------------------------------------------------------------------------------------------------------------------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|86038682|gb|DR334437.1|DR334437EST: TAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTG ATGGGAACTGGGTTTAGCATCCTGATATCAAAAAGAAATCCTTCGTTGGTC
genomic: TAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccct ... ctatgtgaagATGGGAACTGGGTTTAGCATCCTGATATCAAAAAGAAATCCTTCGTTGGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACGTCTACTCGTACACCGATCTATAAAGCCTTTGCTAAAGGAGAAAACATAGGAGACGTAACTGCTAAAGGAGAGTGTGTTGGTAATATTGCAGATCTGgtatgaccctttttcaacattagttttcattgtttcttgggtgttttgttggtttaatctgtcaagcggaattaaatttgaactaaaggtggctacattgctagtttgctacttgttgcttaagggtcgaaatagattctgtttgatctctttttgagctctaaaattttcatttgtttttattattttctatgtgaag
- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT