Sequence
atgc intronic sequence ATGC exonic sequencegtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43600.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 6
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
||| || || || || ||| || | |||| ||||| | | | || | || |||||| | | || || ||||| || || ||||||||||| |||||| | |||||||| |||||||| ||||| || |||||||| || || || |||||
-----gttggattgtgagttaatt----aataagtttatggaaaattgttcttc--ttatactcat----gtgtgttcttacaacagGTATCAAAATTGGCGTTGTCACTGCTATTGCTGCTCCTGCAAGTATTAAGGTGGAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGC
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
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------------------gtaggttcccagtaaattaacatgtttgcggtttcaagttgatggtatacaagtcttctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G32850.2 (Glycine max), 3'ss of exon 5
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagtta-ataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
|| | | | || | | | ||| | |||| | | ||| | | ||| || || || ||| ||||| || ||| || | || || |||||||| |||||||||||| | | ||| ||||||||||||||||| || ||||| ||||||| |||||||| |
gtacacatcttggagctaacata-atcattgcattggccataatttcaatgatctgatattctgatgtaatatgtttctttacc-cagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G34790.1 (Glycine max), 3'ss of exon 6
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagtta-ataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
|| | | | || | || ||| | ||| | | ||| | | ||| | || |||||| ||||| || ||| || | || || |||||||| |||||||||||| | | || ||||||||||||||||| || ||||| |||||||| |||||||| |
gtacacatcttggagctaacata-gtcatttcattagccataacttcaatgatctgatattctgatgtaatctgtttcttgacc-cagGTATATCTATAGGCATAGTCACTGCCATTGCAGCTCCAGCAAGTCTAACAGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGTCCTTATGCCTAA
upper sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
| ||| || |||| | | ||| | ||| || || | || ||| ||| || ||| || ||||||| ||||||||||| || |||||| | || ||||| ||||||||||||||||| ||||| |||||||| | |||||| |
--gtaggcctctt-tctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAAMapped 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|164140324|gb|EL983157.1|EL983157EST: CTTGAAGACGAAG GTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGG
genomic: CTTGAAGACGAAGgtccggttaa ... ttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
ttttgac putative branch site (score: 3)
tcattttt CT-rich tract
tttcattatagttaat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG