Sequence
atgc intronic sequence ATGC exonic sequenceAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04040.1 |
intron # | 6 |
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 6
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 6
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaa----ctttaaaatttatgcataacttagtt-gtctttttatag-----aagaccttccattttgtgattatatacatgtag-----------
||| | ||||| || |||||||||||||| || || |||||||||||||| |||||||||| ||||| ||||| ||||||||||||||||||||||| | | | |||| | | | ||| | | || || ||||||| || | |||||| || || | || ||
AAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTAAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACTGCTTGCAAGgtgaatgaagatatttactctgtcttcattgttcattttgtaattttatattgttctgacccctacatttttaaatactacaaatatataattattctta
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 6
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaa----ctttaaaatttatgcataacttagtt-gtctttttatag-----aagaccttccattttgtgattatatacatgtag-----------
||| | ||||| || |||||||||||||| || || ||||||||||| || | |||||||| ||||| ||||| ||||||||||| ||||||||||| | | | |||| | | ||| | | | || || ||||||| || | |||||| ||| || | || ||
AAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCTTGCAAGgtgaatgaagatatttactcggtcttcattattcattttgtaattttatattgttctgatccctacatttttaaattctacaaatatataattattctta
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 6
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaacttta-------aaatttatgcata-acttagttgtctttttata-----gaagaccttccattttgtgattatatacatgtag--------
||| |||||||||| || ||||| |||||||| || || ||||||||||| || |||||||||| ||||| ||||| ||||||||||| || |||||||| | | | || | || || | ||||| | | || |||| | | | | | | | || | | | ||
AAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCATGCAAGgtgaatgaagctatgtagtcagccttctgtgtgcacttattattattattattattatgggaatatcctaccatataatcagggagtttgagagaatcgg
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 4
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaacttta-------aaatttatgcataacttagttgtctt----tttata--gaagaccttccattttgtgattatatacatgtag--------
||| |||||||||| || ||||| |||||||| || || ||||||||||| || |||||||||| ||||| ||||| ||||||||||| || |||||||| | | | || | || | | || || | | || ||| | | | | | | | | || | | | | | |
AAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCATGCAAGgtgaatgaagctatgcagtcagccttctctgtgcatttattattatgtgattaataatgggaatatcctagtatataatcagagagcttttgagagaatc
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 6
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagt--aactttaaaatttatgcata-acttagttgtctttttataga--agaccttcca---ttttgtgattatatacatgtag-------------
||| |||||| ||| ||| ||||||||||| ||||| || ||||||||||| || |||| || || ||||| ||||| || ||||||||||| |||||||| | | | | | | | | | || ||||| ||| | | || | ||| | || |||| | | || | | ||
AAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCATGCAAGgtgattctacatatccattcaacgtttacacttacaaatctgtgtgtacatcagattgtgcacatttttttaaggatctgaagctaattatgtactgaatMapped 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|125306473|gb|EL320558.1|EL320558EST: CAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAG ATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGA
genomic: CAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaact ... atacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT