Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacttacgacttaactgataaatatgtatccagatctctaggaaatgtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10070.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G114758_T01 (Zea mays), 3'ss of exon 6
-----------------gtaagaac----ttacgacttaactgata-aatatgtatccagatctctaggaaatgtttctaatttctttta-tggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
||| | | ||| | ||| | || || || | ||| | | | || ||| | ||| ||| | | |||||||||||||||| |||||||| ||||| || || ||||| | |||||||| | ||||||||||| |||||||| || || | ||| ||||
agaacctatgtaatgaagtaggtcctcttttatggcttcatatatgtaaactggagttggatttgttaaatatatttgtgctttatttaaataattgcagTACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
upper sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
-------------------gtaagaacttacgact--taactgataaatatgta-tccagatctctaggaaat-gtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
| | | || | || | || | | ||| | | || | || || | |||| | || | | | ||||||| |||||| | |||||||| ||||||||||||||||| | |||||| || |||| ||||| |||||||||||||| ||||| | | ||||
atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
upper sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
---------------------gtaagaacttacgacttaactgataaatatgtatccagatctctaggaaat--gtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
||| | | || || | ||| | || | | | |||| | || | | | ||||||| |||||| | |||||||| ||||||||||||||||| | |||||| || |||| ||||| |||||||||||||| ||||| | | ||||
tatttaatctttttgccttgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaataatagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
upper sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtaagaacttacgacttaactgataaatatgtatccagatctctaggaaatgtttcta-------atttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
| || || | | || || | || | | ||| |||| | | | | | | |||||||||||||| | || ||||| || |||||||||||||| ||||||||||| | || |||||||| || |||||||| |||||| | ||||
agagtaatgtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATGMapped 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|19874774|gb|AU235605.1|AU235605EST: TCTAACTGATGTCCCGTTTGCAAAGCTGCGTTGTACTGCACCTCGTCTTT TACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGT
genomic: TCTAACTGATGTCCCGTTTGCAAAGCTGCGTTGTACTGCACCTCGTCTTTgtaagaactt ... atggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatatgtatccagatctctaggaaatgtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
ttctaat putative branch site (score: 2)
tttcttttat CT-rich tract
aaatgtttctaatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacttacgacttaactgataaatatgtatccagatctctaggaaatgtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG