Sequence
atgc intronic sequence ATGC exonic sequenceGCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactctattctcttcattatctggatttctcatatctaatgctcttggaatttttgatttgatag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G15900.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgtta---caactcta----ttctcttcattatctggatttctcatatctaatgctcttggaatttttgatttgatag-----
| || ||||| ||| | || || || ||| | || ||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||| ||| || | | | || ||| || | | ||| || | || | | ||| ||
GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagttttactttaagtatggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag
upper sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactctatt----ctcttcatta---tctggatttctcatatctaa-----tgctcttggaatttttgatttgatag
|||| ||||| ||||| |||||| ||||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||| ||| | || ||| | | ||| | | | | |||| | || |||||| || ||
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagtgactaaattcatatgctatatatttttctttgttcag
upper sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S169_73V6.2 (Physcomitrella patens), 5'ss of exon 8
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactctattctcttcattatctggatttctcatatctaatgctcttggaatttttgatttgatag---------------------------------------------
| ||||| || || ||||||| | || ||||| || ||||||||||| |||||||||||||||||||| |||||| | || ||||| || | || || | || | || | | || | || || | | | |
GTCTCGCAGTGAGTGCTCGACATCCTTACATGTTTTCAGCTGGTGATGATAAGCAAGTCAAATGCTGGGATCTTGAGTACAACAAGgtgtgttctggctccttttaagcatattaatgcgtagcctttacttggctctgagtcagaggtcatttcaaatgtcattttctgagactctactctgggatatgggtttgctcagMapped 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|116453833|gb|EG496425.1|EG496425EST: CTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAG GTTATCCGATCTTATCATGGTCACTTGAGTGGTGTCTATTGCTTAGCTCTG
genomic: CTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactc ... gatttgatagGTTATCCGATCTTATCATGGTCACTTGAGTGGTGTCTATTGCTTAGCTCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactctattctcttcattatctggatttctcatatctaatgctcttggaatttttgatttgatag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG