Sequence
atgc intronic sequence ATGC exonic sequenceGACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
|| || || ||||| |||||||| |||||| ||| ||||||||||||| |||||||| ||||| |||||||||||||| || || ||||||||||||| | | || |||| | | | || || | ||||||| | || | | | ||| ||
TACCAAATCTTTTGGATGGGATACCGTTGATTCTTTCCTGCAGCATGATGTTCAAGAACTGAATCGTGTTCTCTGCGAAAAACTGGAAAACAAAATGAAGgttggacatttatttttgttatat-gtaagataata----aatagtgtttc--atcaatgtacaactactctctcgattcag-----
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 2
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatg-atttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
||| ||||| |||||||||||||||||||| |||||||| ||||| ||||| | |||||||| || || ||||| || || |||||||| | ||| | | | || | || | || | ||||| | || |||| |||| ||| | |
------------TGGATGGGACACATATGATTCCTTCATGCAACATGATGTACAAGAGCTCAACAGAGTTCTCTGTGAGAAACTTGAAGATAAGATGAAGGTGACAAATCT---Ggtatagagctgtatatatgctgcat-gttggctgctattaactttg----ctttcttcctag-----------
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttct---------tttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
||| || || ||||| ||||| || |||||||| ||||||||||||||||| ||||| || || | ||||| || || || ||||| |||||||||||||| | | || | ||| || | | | | ||||| || | | || | |||
GACCAAATCTTTTGGATGGGACACTTATGATTCTTTCATGCAGCATGATGTTCAAGAGCTTAACAGAGTTCTTTGTGAGAAACTTGAAGACAAAATGAAGgtgaatattataacaaacattttattatatgtctacgatttgttattaactttgcgttgacccag-------------------------------
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
||| || || ||||| |||||||| |||||||| ||||||||||||||||||||||||||||| | ||||| || || || || || || || |||||||| | | | | || |||| ||| | | | || | ||| | | || || ||||| |
GACTAAATCCTTTGGATGGGATACCTATGATTCTTTCATGCAGCATGATGTGCAAGAACTCAACAGAGTTCTTTGTGAGAAACTGGAAGATAAGATGAAGgtgaatat---------gacaa-taatgaattatcattacaccaat--ttactttttattaacttttctttctacacag--------
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G071441_T02 (Zea mays), 5'ss of exon 2
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
|| || || ||||| ||||||| |||||||| ||||||||||||||||| |||||| | ||| |||| || || |||||||| ||| |||| |||||||| || | |||| | | || || | || | | |||| || || |
CACCAAATCTTTTGGATGGGATAGCTATGATTCGTTCATGCAGCATGATGTTCAAGAATTGAATAGGGTCCTATGTGAAAAGCTGGAGAACAAGATGAAGgtttgccatccaattttgttgaaaaaaaagc--ctgactgactgactcatattaatgtgcagctattcttctcacag----------
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
||| ||||| ||||| ||||| ||||||||||| || ||||||||||||||||||||||| ||| | ||| | || |||||||||||||| || ||||||||| | ||| || || ||||| | || |||| | || | ||| || | || | ||
GACGAAGTCCTTTGGATGGGACACATATGATTCTTTTATGCAGCATGATGTGCAAGAACTTAATAGAGTTTTATGTGAAAAGCTTGAGGATAAGATGAAGgtatatgaggtttaac-----agctgcagctt-----tcagt-atttttcactgttctgaagttttttattttatattactggacag
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaa-------tttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag-------
||| ||||| || || ||||| || ||||| ||||| ||||| || ||||| || ||||||||||| ||||| || || ||||| ||| | ||||||||||| ||||| | ||| | ||| | | || ||| | || | | || || || | | | | ||| |
GACGAAGTCTTTCGGATGGGACACTTATGAATCCTTTATGCAACACGATGTTCAGGAACTCAATCGAGTTCTGTGTGAGAAGCTAGAGAATAAAATGAAGgtttgcctctccttttcatatgtactttttccacgctcggaaacccaga-gctggtcgtgacagtttagacctgatatggcccactgactgaggtgatatt
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgta-----------atttttcttttgttgtcaggccatgattta-ctactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
|| ||||| || || ||||||||||| || ||||| ||||| |||||||| || || |||||||| |||||||| |||||| | || || |||||||||||| || | | ||||| || | | | | | | || ||| | | ||| | || | | | | |||| | ||
TACTAAGTCTTTCGGATGGGATACATACGACTCCTTTATGCAACATGATGTTCAGGAGCTCAATCGAGTTCTCTGTGAAAAGTTGGAAGATAAAATGAAGgtatggaagaattagttctagtcttgttttcttttctttcctgagttgcgtcgtatgtgatcttaactttgttgtggttctcacctggcctttc-gcag
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 5'ss of exon 6
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgta------atttttcttttgttgtcaggccatgatttactac--tcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
|| || || ||||| ||||| || || || || || ||||| |||||||| ||||| || ||||||||||| ||||| ||||| || ||||||||||||||| | | | || | | | | | ||| | | | | ||| | ||||| | | | || || | ||
CACTAAATCTTTTGGGTGGGACACCTACGACTCTTTTATGCAACATGATGTTCAAGAGCTGAATCGGGTTCTTTGCGAGAAGCTGGAAGACAAAATGAAGgtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacag
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 4
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
||| | ||||||||||||||||| || ||||| || ||||||||||||||||||||| | || || ||| | ||||| ||||| ||||| || |||||||| || || |||| || | | | ||||| | ||||| |
GACTAGATCGTTTGGTTGGGATACGTACGATTCGTTTATGCAGCATGATGTGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAGgt----------ttactgct--------attttcttcacgttaaatgttttctaacaccaagctccactacag--------------Mapped 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|164135218|gb|ES030859.1|ES030859EST: TGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAG GGAACTGTTGTGGAGGGAACAA
genomic: TGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttc ... ttttctgtagGGAACTGTTGTGGAGGGAACAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACAAAGTCGTTTGGTTGGGATACATATGATTCCTTCATGCAGCATGATGTGCAAGAACTCAATCGGGTTCTCTGCGAAAAGCTTGAGGACAAAATGAAGgtaatttttcttttgttgtcaggccatgatttactactcagttggtgtttcttgtttttgagctcttttttcttcgtttttctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC