Sequence
atgc intronic sequence ATGC exonic sequencegtaacgtttgatattgtcttgttttaagtatcacatgtcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31930.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g10050.1 (Oryza sativa), 3'ss of exon 2
------------gtaacgtttgat--attgtcttgttttaagtatcacat--gtcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
| | || || || | | | ||||| || | | || ||| || | | | | | | | ||| | | | | | | |||||||| || ||||| |||||||||||||||||||| ||||| ||||| || |||||||||||||| ||||| || ||| |||||| || ||||
tttagctaaactgggcccttgaatcaatggccaagatttaaagatttcttttaccacaaaataagcaatgcttgtca--catcattggaattgtgcttgtagGTT-GCAAATGTTCAATGTCCTCGTGATACTCATTTTTGGGTTTATGATGATGGTCGCTATGAGGAAGAAGGACAGAACAACATCAAAGGAAAAATCTGGG
upper sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G016858_T01 (Zea mays), 3'ss of exon 2
gtaacgtttgatatt----gtcttgttttaagtatcacatgtcaagaaa--caatcgaatataataaaccttgctt------gtgtgtat-atatct-cagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
| | ||| | | |||| || | | || | | || | || | | | | |||| | || || || | ||| | |||||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||||||||||||||| || || || || |||||| || ||||
-ccatagccaagatttcaagagtcaatttacctacaaagaggcatggagtgcactgtaaaagagttacccttttatctcaccacttgcattatgcttgcagGTTGCAAATGTTCAGTGTCCCCGTGACACTCATTTTTGGGTTTATGACGATGGTCGTTATGAGGAAGAAGGTCAAAACAACATAAAAGGAAAAATATGGG
upper sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G34300.1 (Glycine max), 3'ss of exon 3
-------gtaacgtttga-----tattgtcttgttttaagtatcacatg-tcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
||| |||| ||| || | | | ||||| | | | | | | || |||| | ||| | | | | |||||| |||||||||||||||||||||||||| || |||||||| ||||| ||||| ||||||||||||||||| || |||||||| |||||||||||||||
atcccttttaatctttggatgatcattatcattatcataatatcatgggattatggtattactaaaatcaatataataacctttttctttgaattttcagCTGGCAAATGTACAGTGTCCACGTGATACACACTTTTGGGTTTATGATGATGGTCGTTATGAGGAAGAAGGTCAAAATAATATTAGAGGAAACATTTGGG
upper sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G01470.1 (Glycine max), 3'ss of exon 3
---------gtaacgtttga-----tattgtcttgttttaagtatcacatg-tcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
||| |||| ||| || | | | ||||| | | | | | | ||| |||| | | | | | | | || | |||||| |||||||| ||||||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| || ||||||||| |||||||||||||||
tgatcccttttaatctttggatgatcattatcattatcataatatcatgggattatggtattactgaaatcaatataa-taacctttctttgaat-tttcagCTGGCAAATGTGCAGTGTCCACGTGATACACACTTTTGGGTCTATGACGATGGTCGTTATGAGGAGGAAGGTCAAAATAATATCAGAGGAAACATTTGGG
upper sequence: AT1G31930.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0012g02570.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtaacgtttgatattgtcttgttttaagtatcacatgtcaagaaacaatcgaat--ataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
|| | |||| | | | || | | | | | |||| ||| ||| ||| ||| | || | | |||||| |||||||||||||||||||| || || ||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||||||| | ||||| || ||||
aagcacttagcccatatgatatgattatctgtctttcctaatttggtcttgtagtttgttgtcgatgtgatattaacacttaggtgttta-atgtgt-tcagCTGGCAAATGTACAGTGTCCACGGGACACACATTTCTGGGTCTATGATGATGGCCGTTATGAGGAGGAAGGTCAGAATAATATCAGGGGAAATATCTGGGMapped 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|125092155|gb|EL149978.1|EL149978EST: TTTATATTAACGGTAGGGAGATCACAAAGCTTGAGTTGAGGATTTTAAAG CTAGCAAATGTACAGTG
genomic: TTTATATTAACGGTAGGGAGATCACAAAGCTTGAGTTGAGGATTTTAAAGgtaacgtttg ... tatatctcagCTAGCAAATGTACAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgtcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
aatcgaatataataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgtttgatattgtcttgttttaagtatcacatgtcaagaaacaatcgaatataataaaccttgcttgtgtgtatatatctcagCTAGCAAATGTACAGTGTCCACGTGATACTCATTTTTGGGTATATGACGATGGACGTTATGAGGAAGAAGGGCAGAATAATATCCGAGGAAACATTTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG