Sequence
atgc intronic sequence ATGC exonic sequencegtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatctaattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68920.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G09400.1 (Glycine max), 3'ss of exon 3
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatctaattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
||| | | | || | ||| | ||| || | | || | | | ||||| || | |||| ||||| ||||| || ||||| || |||||||||||||||||||| ||||| || |||| ||||
---------gtaagatt-ttgtgagaacttatctgtaatgaaaatgaagtttttgtatgaagaattttaaattagattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGAATGAAGTTTCTTCAAGATCTTGTACCTGGATGCAGCAAG
upper sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatct--aattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
||| | | | || | ||| | || |||| | || ||| || || | |||| || | |||| ||||| ||||| || ||||| |||||||||||||||||||| || ||||| || |||| ||||
---------gtaagatt-ttgtgagaacttatctgtgat-gaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
upper sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatct--aattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG----------------------------------
||| | | | || | ||| | || |||| | || ||| || || | |||| || | |||| ||||| ||||| || ||||| |||||||||||||||||||| || ||||| || |||| ||||
---------gtaagatt-ttgtgagaacttatctgtgat-gaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
upper sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 3'ss of exon 3
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatt----tttcatctaattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
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gtaagatttttcatgg-atagttttagttttgatagaagcaattctat-tgtcctagtcttggagttaaagctggtggacct-tgatgacagGTAAGAAGGGAAAAGATCAGTGAAAGGATGAAGTTTCTTCAAGACCTGGTACCTGGTTGCAGCAAGMapped 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|116476256|gb|EG518848.1|EG518848EST: CTTGCAGAAAGA GTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTA
genomic: CTTGCAGAAAGAgtacaatttc ... gcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTA
EST:
gi|116476258|gb|EG518850.1|EG518850EST: TACGGGCACGAAGAGGCCAGGCCACAAATAGCCATAGTCTTGCAGAAAGA GTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTA
genomic: TACGGGCACGAAGAGGCCAGGCCACAAATAGCCATAGTCTTGCAGAAAGAgtacaatttc ... gcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgaatagaagctatctcttcttgtatttttcatctaattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
atctaat putative branch site (score: 3)
tatttttcatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatctaattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG