Sequence
atgc intronic sequence ATGC exonic sequenceGCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaatcaaaacctctgcttcacttcacacaataatttactcattcaagttttgattcttttttttttgtggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.1 |
intron # | 19 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaatcaaaacctctgcttcacttcacacaataatttactcattcaagttttg----attctttttttt----ttgtggcag
||| || |||||||| || ||||||||||| ||||| || || || || |||| |||||||| |||||| |||||||||| ||||| || ||||||||||| | | || |||| | | | | ||| | ||| || | || | |||| |||| || ||||||
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtt-tgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 20
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaatcaaaacct----ctg---cttcacttcacaca-ataatttactcattcaagttttgattcttttttttttgtggcag-------------------------
|| || ||||| || || ||||| ||||| ||||| ||||||||||| |||| |||||||| || ||| |||||||||| || || || ||||| ||||| | |||||| || | | || ||||| || || | | | || || | | | | | | | ||||| | ||
ACAGCGGGATCCGCTTATTGAGTACAAGCTTGAAGGCTACAATCTATTCTTGGAGATGATGGCACAGATAAGAAGAAATGTTATTTATTCAATATACCAGgta-tatattaaaccagagctagatattgtatcttcagtttgtgcacacatgtcacacagtacactcaccaattctctatttttatctcacctgcaatgcccttttcctatggcag
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: PP1S9_141V6.1 (Physcomitrella patens), 5'ss of exon 19
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaat----caaaacctctgcttcacttcacacaataat-ttactcattcaagttttgattcttttttttttgtggcag---------------------------------------------------------------------------------
|| || || || | || ||||| || | || || ||||| ||||||||||||||||||||||||| || ||||||| |||||||| | || |||||| | | || | | || ||| | || | ||| || ||||| | ||| | | | | | ||
TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactcgtgctgcgcatacgccctacttgaagtctctagtgaatctttttcattagtgacccagttcctgctgcct-gcgacattaggaggtgaaagttgaccaaaatagtcaccagcatgaaacaaaaattcatagtttaatcgctcaaagttctttcttgcag
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: EFJ08380 (Selaginella moellendorffii), 5'ss of exon 19
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttc-ttcattaaatcaaaacct-ctgcttcacttcacacaataatttactcattcaagttttgattcttttttttttgtggcag----------------
||| | || || ||||||||||| ||||| ||||| |||||||| || ||||| |||||||||| || || | || || |||| | | ||||| || || | | | | | || |||| || || |||| || | | || | | | | |
TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgtctatccttttcatgctccttcgttttggacttccattttgtc-tgtatgtatgaagagcatccacgcgatagtgattgcttgatccgtgtt
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: EFJ15249 (Selaginella moellendorffii), 5'ss of exon 19
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttc-ttcattaaatcaaaacct-ctgcttcacttcacacaataatttactcattcaagttttgattcttttttttttgtggcag----------------
||| | || || ||||||||||| ||||| ||||| |||||||| || ||||| |||||||||| || || | || || |||| | | ||||| || || | | | | | || |||| || || |||| || | | || | | | | |
CCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgtctatccttttcatgctccttcgttttggacttccatttcgtc-tgtatgtatgaagagcatccacgcgatagtgattgcttgatccgtgttMapped 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|116485280|gb|EG527872.1|EG527872EST: TGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAG TTTCAACCAGTGCGGGTAAAGAAGGACGAAGAGAAGAAGTCTCAGAACGGG
genomic: TGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcatt ... tttgtggcagTTTCAACCAGTGCGGGTAAAGAAGGACGAAGAGAAGAAGTCTCAGAACGGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaatcaaaacctctgcttcacttcacacaataatttactcattcaagttttgattcttttttttttgtggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA