Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 5
---------gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
| | || | | || | | || | | | | | | | | || || | | || | ||||||||||||| |||||||||||||| || || || ||||| || |||||| ||||| |||| | ||||| |||||||| |||| ||| || || |
gaattcaggagcattggctgccagtttgaatcgtactcatccgctacagcactatttttgcttgaaatttgaatctatcatattgcatgcaactttgcagGTTGAAGACAGCGAACTTGCTGATGTTGCTGCGGTAAGTGCTGGAAATAACTACGAAATTGGCAACATGATAGCTGAAGCTATGAACAAGGTTGGACGAC
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
-gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagc------aagatggtctaaaggttatgtca----ttggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
||| | | | | | || | ||| | | || |||| | |||| | || || | | | ||| | ||| | || ||||||| |||||||| ||||||||||| || || ||||||||||| |||||| | ||| |||| | |||||| ||||| || |||| || || || ||
gataattgattcccgt--ttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------gtaagtaactattatgcta-aaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
| | | ||| | | | || | || | ||||||| | | | ||| ||| | | || | | | |||||||||| ||||| | || ||||||||||| || ||||| || || || | ||||| |||| |||||||||||||||| |||||| ||| || || |
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctat----------agcaagatggtctaaaggttatgtcat----tggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
|| || | | | | ||| | || | ||| | ||| || | | ||| ||||| || | ||| | | |||||||||||||||| || || ||||| |||||||||||||| || || ||||| ||||| |||| ||||||||| ||||||||||| |||||||| | |
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
|| ||| | || | | | | | |||| || | || | | | ||| || || | | | | ||||||||||||||||||| |||||||| || ||||| ||||| |||||||||| ||| || || ||||| || ||||| ||||||||||| || | |
gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaa-tgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatc-tgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCAMapped 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|164224921|gb|ES153746.1|ES153746EST: AGAAGACTGCAAAGGCTTTGGTTAACGAGCTGAAACTTATGTCTAAGGAG GTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTAAGTG
genomic: AGAAGACTGCAAAGGCTTTGGTTAACGAGCTGAAACTTATGTCTAAGGAGgtaagtaact ... ggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTG
EST:
gi|124842257|gb|EH926694.1|EH926694EST: GACTGCAAAGGCTTTGGTTAACGAGCTGAAACTTATGTCTAAGGAG GTTGAAGACAGTGAACTTGCTGA
genomic: GACTGCAAAGGCTTTGGTTAACGAGCTGAAACTTATGTCTAAGGAGgtaagtaact ... ggaaatatagGTTGAAGACAGTGAACTTGCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
gtctaaa putative branch site (score: 3)
aaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG