Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgtagcatataatcacctgttcttcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
gtatgttgtagcatataat-cacctgttcttcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtc-agTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
||| || | | || | || || || | | || | | | || | | |||| | | || ||| ||||||||| | || || ||||||||||||||| | |||||||| ||||||||||| | || | |||||||| |||||||||||||||||||||||||||
-------gtaaggattactgcctctatgctggttaagctggtat-tgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
gtatgttgtagcatataatcacctgttcttcctatccttctctctgtttag--tcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
|| | | | ||| | ||| | ||| || || | ||| | | | | | |||||| | |||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||||| |||||||| || || |||||||||
--------------gtatgttcttttccttttttaacttaaattagttaagcatcttgttctttgctatttactcttctgtttt----ggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 12
gtatgttgtagcatataatcacctgttcttc-ctatccttctctctgtttagtcagg-atctgagaagtgttcaactttgttttacat-gtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
||||||| | | || || ||||| | | |||| || | | || | | |||||| |||||||||||||| ||||| ||||| ||||||||||| |||||||| || |||||||||||||||| |||||||| || || |||||||||
--------------------gtatgttcttttccctttttaacttaaattagttaagcatcttgttcttgccatttactctcttgtttcggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAGCTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 10
gtatgttgtagcatataatcacctgttcttcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
| | | | ||| | || | |||| || || | | | | | | | || |||||| ||||||||||| || ||||| ||||| ||||| ||||| |||||||| || | ||| |||||||||| ||||||||||| ||| ||| |||||
-----------------gtatgttctattccctttttttttatctggtttgttaaatgtcttgttccctatatactcttctcttttggcagTGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGGTTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCGAGATCTGAG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 13
gtatgttgtagcatataatcacctgttct-tcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
|||||| | | | || | | || ||||| | | | | | | | || |||||| ||||||||||| || ||||| ||||| ||||| |||| |||||||| || | ||| |||||||||| ||||||||||| ||| ||| |||||
--------------------gtatgttctattccctttttttatttggttagttaaatgtgttgtttcctatatactcttctcttttggcagTGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGATTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCTAGATCTGAGMapped 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|19874907|gb|AU235738.1|AU235738EST: ACTTTTGGGCAGTCAGAAGAGCTACGTTGTGTCATTGCTGTTGTTCGACA TGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAA
genomic: ACTTTTGGGCAGTCAGAAGAGCTACGTTGTGTCATTGCTGTTGTTCGACAgtatgttgta ... tacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
ctttgtttt CT-rich tract
tttgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgtagcatataatcacctgttcttcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtcagTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA