Sequence
atgc intronic sequence ATGC exonic sequenceACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtctccataaaacatcgaatggattaattattcgcctcttccttaacaagtcaagagcctacccttatttagccactaaattacag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45540.2 |
intron # | 25 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 5'ss of exon 23
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtctccataaaacatcgaatggattaattattcgcctcttccttaacaagtcaagagcc--tacccttatttagccactaaattacag-------
|| ||||| || || ||||||||||| || || |||||||| || | | || || ||| | | ||||||||||||||||||||||| ||||| | ||| || || | || | || || || | | | | |||||||| | | | || || | | || | |
GCTGCAAGGCGGCAAATTTGATCATGCTGATCGTATGTTTTCTGATCTATCTGGTACATGGGACAGTGTTCTTGAAGACATGAGTGATGTAAAAGAGCTAgtaagtctta---ccagcaatttgttttcctgagtag------gcagcgccgaaatccagtcaagatcttttgctgcaatataactatctgatgatatttatcag
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: GRMZM2G044143_T01 (Zea mays), 5'ss of exon 23
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgt------attggtctccataaaacatcgaatggattaattattcgcctcttccttaac-aagtcaagagcctacccttatttagccactaaattacag---------
||| |||| || || ||||| || || || ||||||||||| || || | || || ||| || | ||||||||||||||||||||||| ||||| | ||| || | || | | | || || ||| ||| | | | | ||| ||||| || | | || | | | || |
ACTGCAAGACGGCAAATTTGACCACGCTGATCGCATGTTTTCTGATCTTTCTGGTACATGGGATAGTGTTCTTGAAGACATGAGTGATGTAAAAGAGCTAgtaagtctaccaacaagtatttgcagtagttcccatcgatct-ttactggttcatggcgaaaccaagtctagg--ttgcagcaatctgattatttgatggtaattcatctag
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: Vv15s0048g01650.t01 (Vitis vinifera), 5'ss of exon 24
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtct------ccataaaa----catcgaatggatta--------attattcgcctct----tccttaacaagtca--agagcctacccttatttagccactaaattacag-----------------------------------------------------------------------
||| |||||||| || ||||||||||| ||| | ||||||||||| || |||||||||||||| ||||| ||||||||||||||||||||||||||| || || |||| | | || ||| | | | | | || || | || | |||| || || || || | | || | | | |||
ACTACAAGGTGGCAAATTTGATCATGCGGACAGGATGTTTTCAGATATTGGCTCTACTTGGAATGGAGTGCTTGAGGACATGAGTGATGTGAAAGAATTGgtatgtgtttgtctgaaattttacagaagcgccatttatttgttcatatgccatatggtttgactttgagctcctcaagtggttgtcagtgcttttgtctcttctgatattcttttatgttaattgctgaatgtggttactacatctccttttttacaagagctaatatatgccttttcataacctcttag
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: EFJ20662 (Selaginella moellendorffii), 5'ss of exon 23
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtctccataaaacatcgaatggattaattattcgcctcttccttaacaagtcaagagcctacccttatttagccactaaattacag
|||||| || || |||||||||||||| || | ||||| ||| || || |||||||||||| | ||||||||||| ||||| |||||| ||||||| | ||| | | || | | | | |||
ACTTCAGGGGGGCAAGTTTGATCATGCGGATAGAATGTTCAGCGACATTGGCTCTACGTGGAATGGAGTTTTGGAAGACATGAGCGATGTAAAAGAACTGgtacg-gtctatctttttggtgtgttttctg----agccttccattttttcag-------------------------------------------
upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 25
lower sequence: EFJ32770 (Selaginella moellendorffii), 5'ss of exon 23
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtctccataaaacatcgaatggattaattattcgcctcttccttaacaagtcaagagcctacccttatttagccactaaattacag
|||||| || || |||||||||||||| || | ||||| ||| || || |||||||||||| | ||||||||||| ||||| |||||| ||||||| | ||| | | || || || | | |||
ACTTCAGGGGGGCAAGTTTGATCATGCGGATAGAATGTTCAGCGACATTGGCTCTACGTGGAATGGAGTTTTGGAAGACATGAGCGATGTAAAAGAACTGgtacg-gtctatctttttggtgtgttttctg----aaccatacattttttcag-------------------------------------------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|47828319|gb|CK118003.1|CK118003EST: CAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTG GTTCCAGAGTTGTTTTACCTCCCTGAGGTGCTGACCAACGAAAATTCGATT
genomic: CAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattg ... taaattacagGTTCCAGAGTTGTTTTACCTCCCTGAGGTGCTGACCAACGAAAATTCGATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTTCAAGGTGGAAAGTTTGATCATGCAGACCGCATGTTTTCAGACTTTCCAGGCACTTGGAATGGAGTTCTTGAAGACATGAGTGATGTGAAAGAATTGgtacgtattggtctccataaaacatcgaatggattaattattcgcctcttccttaacaagtcaagagcctacccttatttagccactaaattacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA