Sequence
atgc intronic sequence ATGC exonic sequencegtagatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 2
gta-gatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaag---ggagttggatttttt---atggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
||| || || | | ||| | | | | || | ||||| | | | | || |||| | ||| ||||| || |||||||| |||||||||||||| || ||||||||||| || | || |||||||| ||||| |||||||||||||||||||| ||||| ||||
gtacaattttaatgcaacatcttttcctttcagtattttttttggtcaactgaggtgatcatatttatatttcatgtgatgtcagGTTGTTGAGGATGGATATGAGTTCTTTGCCGACAGACAACTTGTCACCATATTCTCAGCTCCAAACTATTGTGGTGAATTTGATAATGCAGGTGCAATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
---------------gtagatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaagg---gagttggat---tttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
||| ||| | || ||| || || | | || || | | ||| || | | ||| ||||| || |||||||||||||| || |||||||| ||||| ||||| || | || || || || || || |||||||||||||||||||||||||| ||||
gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G41890.2 (Glycine max), 3'ss of exon 2
-------gtagatatttttcaat---cat---gtctctttgatactactgct---tttgtgatgtt------aacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| | | |||| |||| ||| | ||| | || | | | || ||||| | ||| | || | ||||||| |||| || |||||||||||||| |||||||||||||| |||||||| ||| | ||||||||||| ||||| |||||||||||||| ||||||||||||||||
gtcactcttggtttttttacaatactcattcagcttctctagtaaaaaggttaaacttatgatgctttactggacactgacattataacttttatg-tagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGCAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G07080.1 (Glycine max), 3'ss of exon 2
------------gtagatatttttcaatcatgtctctttgatactactgct---tttgtgatgtt------aacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| | | | ||| ||| || ||| | ||| | | | | |||| | ||| | || | ||||||| |||| || |||||||||||||| |||||||||||||| ||||||| ||| | ||||||||||| ||||| |||||||||||||| ||||||||||||||||
gtcactgtttttttttacaatactcattca-gtttctataataaaaaggttaagcgtacgatgctttactggacactgacattataaattttatg-tagGTTGTAGAGGATGGGTATGAATTCTTTGCTGATAGGAAACTTGTTACGATATTTTCAGCTCCAAACTATTGTGGTGAATTTGACAATGCTGGTGCGATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 3'ss of exon 2
gtagatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| || || | | | | | | | || ||| | ||| | | || || | | |||| |||| ||||||||||| ||||| |||||||| ||||| |||||||| || || || |||||||| |||||||||||||||||||||||||||||||| ||||
----gttattggcatttttagttttctcttgtt-ctattttactcatgctgaaaactgaaattcttcttttggtctagGTTGTGGAGGATGGATATGAATTCTTTGCCGATAGGCAACTTGTTACCGTATTCTCAGCTCCCAACTACTGTGGTGAATTTGATAATGCTGGTGCAATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtagatatttttcaat---catgtctctttgatact---actgc--ttttgtgatgt--taacaagggagttg-----gattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| | |||||| | | | || | ||| | || | ||| | ||| | ||| | || ||| |||| ||| ||||| || |||||||| ||||| ||||| || | | || || || || | || || || || || ||||||||||||||||||||||| ||||| ||||
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatg-cagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------gtagatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| || || | || || | | | || | || | | | | | | || |||| || || ||||| || |||||||| ||||| || || ||| | | ||||| || || | ||||| ||||| || || |||||||||||||||||||| ||||| ||||
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatactatgctgatctgtgtgggatgttacata-cagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtagatatttt--tcaatcatgtctctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
| | | | | | | | || | || || ||| | | ||| | | || || | ||| ||||| ||||||||||| |||||||| |||||| | | || || || || | || || || || || ||||||||||||||||||||||| ||||||||||
gattttacaaattgtacaatgtgattcagtctcctaatgggtagaattaccttattcctggtgtgtttcaagtactgacatgtg---tgaatgtcacatg-cagGTAGTGGAGGATGGTTATGAGTTTTTTGCTAAACGCCAGCTGGTCACTATTTTCTCTGCACCAAATTACTGTGGTGAATTTGATAATGCGGGTGCGATGAMapped 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|124785858|gb|EH875537.1|EH875537EST: CCGAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAG GTCGTGGAGGATGGGTATGAAGTTCTTTGCTGATAGACAACTTGTGACGGT
genomic: CCGAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAGgtagatattt ... tttatggcagGTCGTGGAGGATGGGTATGA-GTTCTTTGCTGATAGACAACTTGTGACGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
tgttaac putative branch site (score: 2)
ttttttat putative PPT
attttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatatttttcaatcatgtctctttgatactactgcttttgtgatgttaacaagggagttggattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG