Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaagcttttcttttttatgattaggctgttgatataattgaggggtcgaagtttaatggaaacgtggaattatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------gtaaaaaaagcttttcttttttatgattaggctgttg----atataattgaggggtcgaagtttaatggaaacgtggaattat--gatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
||||||||| ||| | | ||| || | | | | || ||||| | | ||| | | | || | || |||||||| || ||||||||||||||||| ||||||||||| || |||||| | || ||||| || || ||||| || ||| | ||| || | |||
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 2
-----------------------------------gtaaaaaaag------cttttcttt-tttatgattaggctgttgatataa----ttgaggggtcgaagtt---------taatggaaacgtggaattatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
| |||||| | ||||||||| | || || | || | || ||| || | | | | ||| | || || ||||||||||| |||||||| |||||||| ||||| ||||| ||||| || ||||| || || ||||||| | | | || ||| | | || || | |
gtaaggatttggcagaaatttttataattgaaaaagaaaaaaatgattgttcttttctttgtcggtgcttcatgttttcttgtactagtttgttaagttgtaactgtttttcattcatgtatgtgtctttttcctgcagGTTTGATGCTGTGATACATTTTGCTGGGCTTAAGGCAGTGGGTGAAAGCGTGGATAAACCACTGCTCTACTTTGACAACAACTTGATAGGGACAATCGTT
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 2
--------------------------------------------gtaaaaaaagcttttcttttttatgattaggctgttgatataattgag--gggtcgaagtttaatggaaacgtggaattatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
| ||||| | ||||||| | || || | | | ||| | | | | || || ||||||||||| || ||||| |||||||| ||||||||||| ||||| || ||| |||| || ||||||| | | | || || | | || || | |
gtaaggattaggcagaaattttttataataattgaaaaaacaaagaaaaaagtattgttcttttctttgtcggtgcgtcttgttttcttgtactagtttgtaagttgtaactctgtcttttttcctgcagGTTTGATGCCGTCATACATTTTGCTGGGCTTAAAGCAGTGGGTGAAAGCGTGAAGAAACCACTGCTCTACTTTGACAACAATTTGATAGGGACAATCGTTMapped 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|19878760|gb|AU239591.1|AU239591EST: GTGGATCTCCGAGACAGGCCTGCGCTTGAGAAGATATTCTCAGAAACAAA GTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGT
genomic: GTGGATCTCCGAGACAGGCCTGCGCTTGAGAAGATATTCTCAGAAACAAAgtaaaaaaag ... attatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctgttgatataattgaggggtcgaagtttaatggaaacgtggaattatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
gtttaat putative branch site (score: 4)
ttgatataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaagcttttcttttttatgattaggctgttgatataattgaggggtcgaagtttaatggaaacgtggaattatgatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC