Sequence
atgc intronic sequence ATGC exonic sequenceGAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaattttgcggctgaatcatgattatgtcattgattgtgttttgttagaggactgacagtgcacttttgatgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23850.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g46750.2 (Oryza sativa), 5'ss of exon 4
-GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaat-tttgcgg-------ctgaatcatgattatgtcattgattgtgttttgttagaggactgacagtgcacttttgatgtag--------------------------------------------------------------------------------------------------------
||||| ||||||||||||||||| |||| |||||| |||||||||| ||||||||||| ||| | ||| | | | || |||| | ||| | | | | | | ||| ||| | || |
GGAAGCCGT-TGTGGTATCTATGGTGCTAATTGTCCTGAATGGATTATCACGATGGAGgtaatgttttcaatcttgttctgtagccagcttttgtc-tggatgcactctcatcatttcgcagcaagtaaactgtcaattttcacccattatttagtcatttttgtcttttggggcacttatgttgctgaaacaattgtaacgcttggtacttatgtctcgccaatttatgtttctgtccttttcag
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g46750.4 (Oryza sativa), 5'ss of exon 1
--------------------------------------------GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaat-tttgcgg-------ctgaatcatgattatgtcattgattgtgttttgttagaggactgacagtgcacttttgatgtag--------------------------------------------------------------------------------------------------------
||||| ||||||||||||||||| |||| |||||| |||||||||| ||||||||||| ||| | ||| | | | || |||| | ||| | | | | | | ||| ||| | || |
TTAAAGAATCATACCATCTCATTTTAATTTGATAATTTTGCAGGGAAGCCGT-TGTGGTATCTATGGTGCTAATTGTCCTGAATGGATTATCACGATGGAGgtaatgttttcaatcttgttctgtagccagcttttgtc-tggatgcactctcatcatttcgcagcaagtaaactgtcaattttcacccattatttagtcatttttgtcttttggggcacttatgttgctgaaacaattgtaacgcttggtacttatgtctcgccaatttatgtttctgtccttttcag
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G002614_T01 (Zea mays), 5'ss of exon 4
GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaa----ttttgcggctgaatcatgatt--atgtcatt---gattgtgttttgttagaggactgacagtgcacttttgatgtag-----------------------------------------------------------------------
| ||||||||||||||||| |||| |||||| |||||||||| |||||||||| || || | || ||||| ||||| | ||| ||| ||| | | | || | || | | |
GGTAGTCGTTGTGGTATCTATGGTGCTAATTGTCCTGAATGGATTATCACAATGGAGgtaaaatgttgtgttaccagattttgattcaatgtcttctcatattttgtcttgaaaaaatagatccactaggtttgtattctgaacaaactaaatcactgtgttcataagtttcgcttgtcaaattattaacattaaaatctttatactttgcag
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 4
GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgta-attttgcggctgaatca--tgattatgtcattgattgtgttttgttag---aggactgacagtgcacttttgatgtag------------------
| | |||||||||||| |||||||| |||||| | || |||||||| |||||| ||||| ||||| ||||| | ||| | ||| ||||| | | | | |||| | |||| |
GGTGTAAAATGTGGTATTTATGGTGCCAATTCTGCAGAATGGATTATGAGCATGCAGgtacattttatttttgaatttgcttcccttgttttcttttgagttttttccatcttaatttttctgctcactctatatgttggaggtttctattgtatta
upper sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 4
GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaattttgcggctga--atca---tgattatgtcattgattgtgttttgttagagg-------actgacagtgcacttttgatgtag-----------------------------------------------------
| || | |||||||||||||||||| |||||| |||||||||| || |||||||||||| | || | | ||| | || || || | | ||||| || ||| | | ||| ||||
GGAGGACGATGTGGTATCTATGGTGCTAATTCTGCTGAGTGGATCATGAGCATGGAGgtattctttcctcctcccatctctttccttttgctcctgcctttcttttgctactaccgctgttgttgaagttatattttctatgttactatattttgcctctctctatggttttgatttaatgctgcaaggctaatgcagMapped 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|164064240|gb|ES144833.1|ES144833EST: TTATCAGCATGGAG GCTTGTAATGCACATGGACTCTATTGTGTACCGTTATATGATACACTAG
genomic: TTATCAGCATGGAGgtaattttgc ... tttgatgtagGCTTGTAATGCACATGGACTCTATTGTGTACCGTTATATGATACACTAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGCAAAATGTGGTATCTATGGTGCAAATTCTCCTGAGTGGATTATCAGCATGGAGgtaattttgcggctgaatcatgattatgtcattgattgtgttttgttagaggactgacagtgcacttttgatgtag
- - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - CATGGA