Sequence
atgc intronic sequence ATGC exonic sequencegtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
-------gtacgaaacaa-ctatcgaaatatccgttaatatgaccttttccgtaactatacag-ataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| ||| | || || | || | || || || | | | || | ||| | | ||| ||| | | || |||||||||| ||||| || || ||||| || |||||||| |||||||||||||| ||||| | || || | |||| ||||| || || || ||
acttggatcagcaaatattctgtctgtagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgt-gagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
-gtacgaaacaactatcgaaatatccgt--taatatgaccttttccgtaactatacagataaaatg---acactgt-ttgtgtttgttg-tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| || || | | | || | || | || | | | | ||| || | | | ||||| || | || || |||||||||| ||||| || || |||||||| || ||||| |||||||||||||||||||| | || ||| | ||||| ||||| || || || ||
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatg---acactgttt----gtgtttgttgtatgat----ctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| | | | | | | | | || | || | | | | || || | | | ||| | || || ||| ||| | ||||||| || |||||||| || |||||||| || ||||| |||||||||||||||||||| | || || | |||| ||||| || || || ||
--atcatgtgattgtacagct-tatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 11
-----gtacgaaacaac-tatcgaaatatccgttaat-atgaccttttccgtaactatacagataaaatgacactgt---ttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
||| | | ||| || | | ||| | |||| | | | | ||| || || || | ||| || ||||| | ||| || |||| || || | || || ||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||| |||| ||||||||||||||||| ||||
tataagtatgtcctattatatggacttgtttgttttttatgagcatataaat--ctaaacctttatgattcaattgtggtttttgtttctattatcatgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 19
------------gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| | | || || | || | | ||||| | | | | || | | ||| | | ||| | | || || |||| || || | || || ||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||| |||| ||||||||||||||||| ||||
ctcaagatcttggaaagtggaaagcttctagctacctgagaatataaatctaaacctctctgatttgcttcaattatggttcctgtttctcttc----atgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataa---------aatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| | || || | || | | ||| || | ||| | ||| || | | || | | | | ||| | ||| || |||| || || |||| || ||||| ||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| |||||||| |||||||| ||||
-cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 17
----------gtacgaaacaactatcgaaatatccgttaatatgacct-tttccgtaactatacagataaa-atgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
|| || | || | | | || | | || | |||| | || | | || | ||| || |||| |||| ||||| |||||||| |||||||||||| | ||||| ||||||||||||||||||||||| |||||||| |||| |||||||| || || || ||||
aacactcactttaggaggctctcatttgtcagtttctaactaacatgtgctttcagaacttttggaatggatgagtcattattttctttctttgtgg----cagGGGACAAGTAGGCCTGCTCATTACCATGTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATG
upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 18
gtacgaaacaactatcgaaatatccgttaatatgacctt---ttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
| || || || | | ||| || | | ||| | || ||| ||| | ||||||||||||| || ||||| || || || ||||||||||||||||| ||||| || ||||| | || || || || |||| || || || || || |
---------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagact---------------atgttacagGGAACAAGCAGACCAGCACACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACGMapped 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|164068023|gb|ES138854.1|ES138854EST: GCCATGCGGGTATTCAG GGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTA
genomic: GCCATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTT-
EST:
gi|124716615|gb|EH808017.1|EH808017EST: ATGCGGGTATTCAG GGAACAAGCAGGCCTGCGCATTACCATGTTCTTTGGGACGAGAACAATTTC
genomic: ATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTC
EST:
gi|164006274|gb|ES130508.1|ES130508EST: GCCATGCGGGTATTCAG GGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATT-C
genomic: GCCATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
ccgtaac putative branch site (score: 3)
tatacagataaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG