Sequence
atgc intronic sequence ATGC exonic sequencegtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17220.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 3
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgt-agcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
|| || || | || || | | ||| | | | || ||| | |||| | | |||| || || || | | || |||||||||||||||||||||||||| || || | || ||||| || |||||||| || |||| |||||||| ||||||| ||||||||||| ||||
-----------------------------------------------------------------gtatagcaaaagtatatgtatattttaccatatgttctctctttctggt-tgtattaacgtggg-------gcattacaactcctaattcttcaacaacaa-tagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40370.1 (Glycine max), 3'ss of exon 3
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
| || || | | | | || | | | | | | |||| | ||| | | ||| | | || | || |||| || | ||||||||||| |||||||||||||| |||||| | || || |||||||| || ||||| || |||||||||||||| ||||||||||||||||||||||| |
----------------------------------------------------------------tgtagtttttaactgaattattaactataactataagtaatcttttcactttcatttcc-----tttagaagtctagatgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGTGGAGCAAGCGTAACAGACATTGCTATTATTGTTGTGGCTGCTGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 4
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
|| || | | || ||| | || | | | | ||| | |||| | ||| | | |||||| | || ||| |||| || | ||||||||||| ||||||||||||||||||||| | || || ||||| || || ||||| || ||||| |||||||| ||||||||||||||||||||||| |
--------------------------------------------------------------tgtagtttttagccgaattattaactataac-tataactcaact-tttcactttcatttcctttagaagtatagttg-atatatatta----tatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGCGGAGCAAGTGTTACAGACATGGCTATTATTGTTGTGGCTGCCGATGATGGGATTCGTCCTCAAACAAATGAAGCTA
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 3'ss of exon 3
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattat-acttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttact-catcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
|| || | || | | ||||| | | | | | | | | | | || ||| | || | ||| || || | || | | || | |||| ||||| || ||||||||||| |||||| | || || |||||||| || ||||| || ||||||||||||||||||||||||||||||||||| || |
-------------------------------------------------------------aaccatcattttaccatttttctaatg-gccttttataaactcaattttgagcttcaatttccttgcttgagataattctattatgtcctcccctt---------tgaagGCGTTTGGGGCGATGAGAGCTCGTGGAGCAAGGGTTACCGACATTGCTATTATTGTTGTGGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAGGCCA
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26137 (Selaginella moellendorffii), 3'ss of exon 3
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
| ||||| | | | || ||| | | | || | | || || || | | | ||| | |||| || |||| ||| ||||||| || |||||| |||| ||||||||||| || ||||| || || |||||||||| ||||| || || |||||||
---------------------------------------------------------------------------------------------gtacatattg--tgttttacgtct-tctttggaaatgctaaaggctttcttgttct----------cgtcaac-agGCTTTCAGTGCTATGCGAGCTCGTGGTGCACGAATCACAGACATTGCAATTATCGTGGTAGCAGCAGATGATGGAACCCGTCCACAGACTTTGGAAGCAA
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ10805 (Selaginella moellendorffii), 3'ss of exon 3
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
| ||||| | | | | ||| | | | || | | || || || | | | ||| | |||| || |||| ||| ||||||| || |||||| |||| ||||||||||| || ||||| || || |||||||||| ||||| || || |||||||
---------------------------------------------------------------------------------------------gtacatattg--tgttttatgtct-tctttggaaatgctaaaggctttcttgttct----------cgtcaac-agGCTTTCAGTGCTATGCGAGCTCGTGGTGCACGAATCACAGACATTGCAATTATCGTGGTAGCAGCAGATGATGGAACCCGTCCACAGACTTTGGAAGCAAMapped 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|47831587|gb|CK121271.1|CK121271EST: TTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATACTCCTGGACATGAG GCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATC
genomic: TTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATACTCCTGGACATGAGgtagattctt ... cctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATC
EST:
gi|125012884|gb|EL085153.1|EL085153EST: ACTCCTGGACATGAG GCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCTATC
genomic: ACTCCTGGACATGAGgtagattctt ... cctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
atcttac putative branch site (score: 3)
tcctcatct putative PPT
ttacttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgtagcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA