Sequence
atgc intronic sequence ATGC exonic sequenceATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttctcaaagttttatatttccgtctctttctgactgtttttttacttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56290.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os08g39080.1 (Oryza sativa), 5'ss of exon 12
ATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttct--caaagttttatatttccgtctctttctgactgtttttttacttgcag-------------------
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GCTGCAGCTGAAACCACAAGACTATTCTCTCTGGAATAAGCTAGGTGCGACCCAAGCAAACAGCATCCAGAGTGCTGATGCAATATTGGCCTATCAACAGgtaattagttattgtaagatattttatttttcagctttggtgaatgtttcgctataagtgctatagcgtatttacatatctctactactgtaaaagcaga
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G080775_T01 (Zea mays), 5'ss of exon 12
ATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttc---tcaaagttttatatttccgtctctttctgactgtttttttacttgcag------------------
| |||| || |||||| | || ||||| || ||||| ||||| |||||||| ||||| ||||| |||||||||||||||| |||| || ||||| ||||| | || | | | || ||| ||| | | || |||| | | | | || |
ACTACAGCTCAAACCACAGGACTATTCACTCTGGAACAAGCTTGGTGCAACCCAAGCAAACAGCATCCAGAGTGCTGATGCAATATTGGCGTATCAGCAGgtaattagctcaggaacatgtttaatgtttcaacgttggtctttttgcccgcacagctagctgaatttgtatatattcctgcttatatcgtgtctgatgc
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G115855_T01 (Zea mays), 5'ss of exon 12
ATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttc----tcaaagtttt-----atatttccgtctctttctgactgtttttttacttgcag------------
| |||| || |||||| | || || || || ||||| ||||| |||||||| ||||| ||||| |||||||||||||||| |||| || ||||| ||||| || | | | | ||| | |||| | | | || |||| | | || || || ||
AGTACAGCTCAAACCACAGGACTACTCACTCTGGAACAAGCTTGGTGCAACCCAAGCAAACAGCATCCAGAGTGCTGATGCAATATTGGCGTATCAGCAGgtaactagctcagaaacatgtttactgtttcaacgttggtctttttgcccacacaactagctggatctgtatatattcttgtttatagatgccttacatg
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv19s0015g01940.t01 (Vitis vinifera), 5'ss of exon 12
ATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttctcaaagttttatatttccgtctctt---tctgactg---tttttttacttgcag----------------
|| |||| || ||| ||||| || || ||||| ||||| |||||||| ||||| |||||||| ||||| || ||||| |||| |||||||||||||| | || || | | ||| | || || | | || | | | | || || || ||
TTTGAAACTCAAGCCACGTGATTACTCCCTTTGGAACAAGCTTGGTGCAACACAAGCTAACAGTGTTCAGAGCGCAGATGCAATATTAGCTTATCAACAGgtag-gcctcacacaattacttttgtactccaattggtcttgttgatagacacattaaacttaattaaatctattgtatttatagaacatttggagtctgaMapped 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|124889585|gb|EH968487.1|EH968487EST: AACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAG GCTCTAGATTTAAAACCAAATTATGTTCGTGCTTGGGCAAACATGGGAATC
genomic: AACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttct ... ttacttgcagGCTCTAGATTTAAAACCAAATTATGTTCGTGCTTGGGCAAACATGGGAATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTACAACTAAAACCAAACGATTATTCTCTGTGGAATAAGCTAGGTGCAACGCAAGCCAACAGTGTCCAGAGTGCTGATGCCATATCTGCTTATCAACAGgttctgttctacgcacagaaatcaaaacttctcaaagttttatatttccgtctctttctgactgtttttttacttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT