Sequence
atgc intronic sequence ATGC exonic sequenceTACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatctataatggtcaattcgagtctagtccctatatttgtgttcttcaacgttcatctattatgatccattggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04040.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 9
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatctataatggtcaattcgagtctagtccctatatttgtgttcttcaacgttcatctattatg-----atccattggcag-------------------------------
|| || |||||||| || | || | |||| |||| || || ||||||||| || ||||||||| | ||||||||||||||||||||||| ||||||||| | || || | | | ||| || || | | | | || | | | |||| || | |||| | | |||
CACTGACTACATTGTTAATATCATTTCTAAAAGAGCTGAGGATAATTATAACTATGGGGTCATTCTTATCCCTGAAGGTCTAATTGATTTTATTCCTGAGgta----gcta-tcactagttgtcaatagtttttttctccccatatgatgttttggcatctgttcacgtacaatcaatatggaaacacctattaatgatggtcacttttatattcttttttgtttgcag
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 9
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatctataatggtcaattcgagtctagtccctatatttgtgttcttcaacgttcatct-attatgatccattggcag----------------------------------------------------------
|| || | || || || || | | |||| |||| |||| | ||| ||||| |||||||||||| | |||||||||||||||||||| || |||||||||| | | || | | | | | || | | | || ||| || ||| | | || | | | | ||| ||
CACTGACTATATCGTAGACGTTGTTTGTAAAAGAGCTGAAATTAATTACAACTATGGTGTCATTCTTATCCCTGAAGGTCTAATTGATTTCATACCTGAGgtatctatcactttgcacagttttcacaatttttttacttgcatttccc---tttatgcacttggaattatattttagtgctgttcatgtacaaccagtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 7
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgta--tatggttactctcaaatctataatggtcaattcgagtctagtccctatatttgtgttcttcaacgttcatctattatgatccattggcag--------------------------------------
|| || |||||||| || | || | |||| |||| || || ||||||||| || ||||||||| | |||||||||||||||||||| || || |||||| ||| || || ||| | | | | | | | | | | ||||| | || ||| ||| | ||
CACTGACTACATTGTTAATATCATTTCTAAAAGAGCTGAGGATAATTATAACTATGGGGTCATTCTTATCCCTGAAGGTCTAATTGATTTCATTCCCGAGgtagctatcactagtcgttaata-gtttttttttctccccatatgatgttttggcatctgttcatgtacaatcaa-tatggaaacatgttaatgaataatgatggtcacttttatattcttttttgcttgcag
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 9
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatct--ataatggtcaattcgagtctagtccc-----tatatttg----tgttcttcaacgttcatctattatgatccattggcag-----------------------------------------------
||||| | || || ||||| | | |||| |||| |||| | ||| || || ||||| |||||| | || ||||||||||||||||| || |||||||||| | | ||| | | | | | ||| | || | | | || | | ||| | | || | ||| || || | | | | |
CACAGACTATATCGTAGATGTTGTTTGTAAAAGAGCTGAAATTAATTACAATTATGGTGTTATTCTTATCCCCGAAGGTCTAATTGATTTCATACCTGAGgtatcta-tcactttgcagttttcacaattatttttttacctgtgtttccccctctgcacttgggattatgttttagtgttgttcatgtacaacctgtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 9
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatctataatggtcaattcgagtctagtccctat-----atttgtgttcttcaacgttcatctattatgatccattggcag--
|||||| ||||||||||||| ||| ||||| |||||| |||||| ||||| ||||| || ||| |||| ||||| || |||||||| || ||||||||||| || | || || | | || | | | ||| | || || | ||| | | | | | || | || ||
TACAGACTACATTGTTGATGTTGTCTGCAAACGTGCAGAACTTGGTTACAACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatattgattataagacttatttatttaacccttttttttgtcctcttgtgaatgggtatccttttaagcaaacttgtcttgctttttttcaagttMapped 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|124797230|gb|EH886909.1|EH886909EST: TTCCTGAGGGTCTAATTGATTTTATCCCTGAG GTCCAACAGCTTATTTCCGAACTGAATGAAGTCTTAGCCGAAGGAAACGTC
genomic: TTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggtt ... ccattggcagGTCCAACAGCTTATTTCCGAACTGAATGAAGTCTTAGCCGAAGGAAACGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACAGATAACATTGTTGATGTGATCTATAAACGAGCAGAAAATGGTTATAACTACGGTGTCATTCTTGTTCCTGAAGGTCTAATTGATTTTATCCCTGAGgtatatggttactctcaaatctataatggtcaattcgagtctagtccctatatttgtgttcttcaacgttcatctattatgatccattggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG