Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttatctctctatctcataagtgaagttctcttgataacttactcataatgtttttatatctttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28080.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G37180.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtaagcttat---ctctctatctcata-agtgaagttctcttgataacttactcataat--gtttttatatctttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
| || | | | |||| || ||| | || | ||| || || | || || || | | | |||||||||||||| || |||||||| ||||| ||||| || ||| |||||||||||||||| || || ||| | ||||||||| | || ||||| |||
gtaagttctttagttgcaactacattattttctgtccaccattcatttttgtgcattttagatcttgtatagttgaattggttcttcttctttctgatcttcacttgttttaattgtgaaatagGTATAGGCTAAAGCACAAGAGAGTTAACATCAGAGCAGTGAAGCATTGGTGTAGACAGATCTTGAGCGGACTTCTCTATCTTCACAGTCACGACCCGCCT
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G30210.1 (Glycine max), 3'ss of exon 3
-----------------------------------------gtaagcttat---ctctctatctcat--aagtgaa--gttctcttgataacttactcataatgtttttatatctttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
| || | | | |||| | | |||| ||| | | | || ||| | ||| || | ||| |||||||||||||| || |||||||| ||||| ||||| || ||| |||||||||||||||| || || ||| | ||||||||||| || ||||| ||
gtaagttcttcagttgcaactacattatttctgttcatcattcacttttgtgcgttttagatcttgtgtagttgaattgtttcttcttcattctgatcttaacttgttt-taattgtcaaatagGTATAGGCTAAAGCACAAGAGAGTTAACATCAGAGCAGTGAAGCATTGGTGTAGACAGATCTTGAGCGGACTTCTCTATCTTCATAGTCACGACCCACCG
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G40550.1 (Glycine max), 3'ss of exon 1
--------------------------------gtaagc-ttatctctctatctcataagtgaagttctcttgataacttactcata-atgtttttatatctttcat----gcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
| | | ||||| | | | | | |||||| | || | || || | || | ||| | | | || |||||||||| ||| || |||||||| ||||| || || || ||| |||||||||||||||| | ||||| | ||||||||||| |||||||| |||
gtgagttccctccattttcatccttattatatatgatcattatccattttgagcttttgagaagttgttttatttttttcttcttttatttatttgttttaattatcacaatagGTATAGGCAAAAGCACAAGAGAGTTAACATTAGGGCAGTGAAGCATTGGTGTAGACAGATCCTGAGAGGGCTTCTCTATCTTCATAGCCATGACCCACCT
upper sequence: AT5G28080.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g03380.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------gtaagcttatctctct-atctca-taagtgaagttctcttgataacttactca-taat----gtttttatatctttcatg-cagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
| ||| | ||| |||| | || || | || || | | | ||| |||| || | ||| || ||||||||||||||||| | |||||| ||||| ||||| || ||| ||||||| |||||||| ||||| || | ||| || || | ||| | || |||
gtaagtatcatacaagttccatgattatgaatgcctttttttttttttgttcaatttctcttgattttctgatctgggcatgttgagaatttgtgtaaattctgtgagcaattttcattttcatttattttgtggtagGTATAGGCTAAAACACAGGAGAGTTAACATCAGAGCTGTGAAGCATTGGTGCAGACAGATCTTAAGGGGGCTGCTCTACCTCCACAACCATAAACCCCCTMapped 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|19876452|gb|AU237283.1|AU237283EST: CGAAACATCAACTTTGTCACTGAAATGTTCACTTCTGGCACCTTGAGACA GTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTG
genomic: CGAAACATCAACTTTGTCACTGAAATGTTCACTTCTGGCACCTTGAGACAgtaagcttat ... tttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataagtgaagttctcttgataacttactcataatgtttttatatctttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
aacttac putative branch site (score: 2)
tttttatatctttc putative PPT
ataatgtttttatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttatctctctatctcataagtgaagttctcttgataacttactcataatgtttttatatctttcatgcagGTATAGGCTAAAACATAAGAGAGTGAACATAAGAGCGGTAAAGAATTGGTGTAGACAGATTTTAAGAGGATTAAACTATCTTCATACACATGACCCTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT