Sequence
atgc intronic sequence ATGC exonic sequencegtatgtacatcttattatttggtgtacaagggttttacatctgctttagtcttttccaatatattgatggcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52920.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 3
-------------gtatgtacatcttattatttggtgta-caagggttttacatctgctttagtcttttccaatatattgatggcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
| | || | | | || | || | | || || | | | || | | | | | ||||||| | | || || | ||||||| ||||||||||| |||| ||||| || || |||| || || |||||||||||| ||||||| || ||||| || || ||| | |||||||||||
cttcttttctgctttgagatgattgtgtattctgatataacttcgattctata-cggtttcatgatgtgct--tttattgatcgatatgttgataccatttagGTGGAATGATGTCGTTGTTGGTCAAGTCCAAAACTGAAGATTCGGTAAAATGTGAAGTTATTGATGGAGGTGAACTGAAATCCAGGCGTCACCTGAATGT
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 3
--------gtatgtacatcttattatttggtgtacaagggttttacatctgctttagtcttttccaatatattgatg---gcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
|| | | || | | | | || || | ||| | ||| |||||| | ||| |||| |||||||||||||||||| || |||| ||||| ||||| | || ||||| |||||||||||||||||||| ||||| || |||||||||||||| |||||||
atttagcattactgttgttggacaatatctttagtatcctgtatatctcagaaagagttaatgccaggtctttgatgcatactatttgtgtatgatgtagGTGGTATGATGTCTTTGGTGGTTAAGTCTAAGACAGAGGATTCTGTGAAATGTGAAGTTGTTGATGGAGGAGAGCTCAAGTCAAGGAGACATTTGAATGT
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 3
gtatgtacatcttattatttggtg-ta-caagggttttacatctgcttt------agtcttttccaatatattgatg---gcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
||| || | |||||| || || | || | || | || ||| | || |||||| | ||| |||| |||||||||||||||||| || |||| ||||| ||||| | || ||||| |||||||||||||||||||| ||||| || |||||||||||||| |||||||
ttatatatttaacattattgggcaatatctttagtatcctatttatcttggaaagagttaataccgggtctttgatgtatactatttgtgtatgatgtagGTGGTATGATGTCTTTGGTGGTTAAGTCTAAGACAGAGGATTCTGTGAAATGTGAAGTTGTTGATGGAGGAGAGCTCAAGTCAAGGAGACATTTGAATGT
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 3
-----gtatgtacatcttattatttggtgtacaagggttttacatctgctttagtcttttc-caatatattgatggcgctt-----ttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
|||||| ||| | || | || | | | || | ||| | | | ||| |||| || | || |||||||||||||||||| | | || ||||| ||||| || || ||||| |||||||||||||||||||| ||||| || ||||||||| |||| |||| ||
tttatagttgtacaatatatccacttgtcttttgttattaaaaaaaggtttgaacttttgagtgaaaaggtaatgatgcttactctttgatgtgatgtagGTGGTATGATGTCAATGGTTGTTAAGTCTAAGACAAAGGATTCTGTGAAATGTGAAGTTGTTGATGGAGGAGAGCTCAAGTCAAGGCGACATTTGAACGT
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 3
---------gtatg-tacatcttattatttggtgtac--aagggttttacatctgctttagtcttttccaatatattgatggcgcttttac-tatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
|||| || ||| || | | ||| | || | || | | || ||| || | | | |||| | | || ||||||||||||||||| | | || ||||| ||||| | || ||||| |||||||||||||||||||| ||||| || ||||||||| |||| |||| ||
cttatagttgtataatatatccacttgtgttttgttcttaaaaggttggaactt--ttgagtgaaaaaggtaatgattcttactctttgatgtgtgacgtagGTGGTATGATGTCTATGGTTGTTAAGTCTAAGACAGAGGATTCTGTGAAATGTGAAGTTGTTGATGGAGGAGAGCTCAAGTCAAGGCGACATTTGAACGT
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 3
----------gtatgtacatcttattatttgg---tgtacaagggttttacatctgctttagtcttttccaatatattgatggcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
| || | | | | || || | | | | | | | ||| || ||| | || | || ||||| | |||||||||||||||| || ||||| ||||| ||||| ||| || || ||||||||||||||||||||||||||||| ||||| || || || || |||||
aaaatgttctgaatatgaagatcaacatgtgaaatcatttgaagcaataaaaatttcttatgtgatttttgaagcccc--tgactctggatctatgctatagGTGGTATGATGTCATTAATGGTCAAGTCCAAGACTGGAGATTCAGTGAAATGTGAAGTTGTTGATGGTGGAGAACTCAAGTCTAGAAGGCATCTAAATGTMapped 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|116479876|gb|EG522468.1|EG522468EST: TGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATG GTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAAT
genomic: TGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATGgtatgtacat ... tatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAAT
EST:
gi|86057128|gb|DR352885.1|DR352885EST: TGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATG GTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAAT
genomic: TGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATGgtatgtacat ... tatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacatctgctttagtcttttccaatatattgatggcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
tattgat putative branch site (score: 3)
cttttact putative PPT
ttttccaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtacatcttattatttggtgtacaagggttttacatctgctttagtcttttccaatatattgatggcgcttttactatgttgtagGTGGTATGATGTCGTTTATGGTGAAGTCAAAGACCAAAGACTCTGTCAAATGTGAAGTTGTTGATGGTGGAGAACTTAAGTCAAGGAGACACCTGAATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA