Sequence
atgc intronic sequence ATGC exonic sequencegttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
--------------------------------------------------------------------------------------------------------------------gttat-tttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
| | | | || || | || | | | || || |||| | || ||| ||| || | | ||||||||||||||||| || ||||| || ||||||||||| ||||| | ||| | ||||| |||||||||||||| ||| |||||||| | || || |||
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgca-tgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
-------------gttatt-ttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaa---attgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
||| | ||| | || |||| || | | ||| | | ||| || || | | | | | || | ||||||||||||||||| |||||||| || |||||||||||||| || ||||| | ||||| |||||||| ||||| || |||| ||| | || ||| |
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattg-cagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
----------------gttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
| | | | | || | ||| | | ||| |||| | || ||| ||| || | | ||||||||||||||||| |||||||| || ||||||||||| || || | ||| | ||||| |||||||||||||| || |||||||| | || || | |
ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
----------gttattttcgcatcttttttttgt----ttactgtgtcaatgagaaa---attcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
| ||| ||| ||| || ||| ||| | || | || || | | | | | | | |||| ||||| ||||||||||| |||||||| || ||| |||||||||| || ||||| | ||||| |||||||||||||| || |||| ||| | || ||| |
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttg-cagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
-------------gttattttcgcatcttttttttg-tttactgtgtcaatgagaaaattcatcatgtggct--ttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
| || || | ||| ||| || ||| | | | | || || | || | || | | | ||||||||||||||||| ||||||||||| ||||||||||||||||| | ||| | |||||||| |||||||||| |||| | ||||| | || ||| |
atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgatttaaagaaagagacacatatctaatcctgtttgatcaacactatatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
---gttattttcgcatcttttttttgtttactgtgtcaatga------gaaaatt-----catcatgtggctttaaattgcctt-tgacttgtcat-cagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
|| || | | | || | | | | ||||||| | || || | | ||| | || | || | ||||| | |||||| || ||||| || || ||||||||||||||| | ||| | |||||||| ||||| ||||||||| ||||| | || | | |||
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAGMapped 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|125261903|gb|EL275988.1|EL275988EST: CAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG GTTAATCCAAAAGCAGCTGAATCTTTAGCTGAT
genomic: CAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttcg ... ttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
ctttgac putative branch site (score: 4)
tttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG