Sequence
atgc intronic sequence ATGC exonic sequenceTGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaacatttggactattgttgttagctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G11910.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g44130.1 (Oryza sativa), 5'ss of exon 1
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaag---------caacatttggactattgttgttagctgtgg---ttgagat--acttttgagtagaaaactaattgtgttctatctcttttgcag------------
||| ||||||| |||| ||||| ||||| || || ||||| |||||||| |||||||| ||||||||||| || || | || ||| ||| || ||||| ||||| || | | | ||| | || ||| ||| | || ||| ||| | || | ||| |||||| |
TGGGGAGATCGGAGTTGGCTGCCCACCGCAGAATTTTACGGTGGTCTTTGACACCGGGAGCTCCAACCTCTGGGTCCCTTCCGCCAAGTGCGTTTTTTCGgtaagaagctacggcaacacatgttttttcttccttacttttgcattttgggattcatgttatgctaggttgataactcacttatttcttttttgctgttgtgggaacag
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G11670.1 (Glycine max), 5'ss of exon 1
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaag-caacatttggact-attgttgtt--agctgtg-gttgagatactttt----------gagtagaaaactaatt----gtgttctatctcttt--tgcag
||||| || ||||||||||| || |||||||||||||||||| |||||||||| || |||||||| | |||||||||||||| ||||| || ||||| || || | ||| | | || || | | || || || | ||||| | | |||| || ||||| | | || |||||
CGGTGAAATAGCCATTGGTACCCCTCCTCAGAAGTTCACTGTGATTTTTGACACCGGTAGCTCTAATTTGTGGGTGCCATCATCCAAATGTTACTTCTCGgtgagattgcttttcaattcataaccgtctaatcaatgcgtgtaggttctttttttcctcctcattttggcaacttgttcatggtgtttttgcatgttggtgcag
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G00810.1 (Glycine max), 5'ss of exon 1
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaacatttggactattgttgttagctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag--------------------
|||||| || ||||||||||| || |||||||||||||||||| |||||||||| || |||||||| | |||||||| ||||| ||||| || ||||| || || ||| | ||| | || | || | || | ||| | | | || | || || || |
TGGTGAAATAGCCATTGGTACCCCTCCTCAGAAGTTCACTGTGATTTTTGACACCGGTAGCTCTAATTTGTGGGTGCCGTCATCCAAATGTTACTTCTCGgtgagattgcttttta--attcataataaccgtcttatcaatgcgtttatttttttatccctcagtttggtaacttgttcatggtgttttgcatgttggtgcag
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G39240.2 (Glycine max), 5'ss of exon 2
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaag---caacatttggactattgt---tgttag-ctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag----------
|||||| || || ||||| || | ||||| ||||||||||| |||| |||||||| |||||||| | ||||| |||||||| ||||| ||||| || || | ||| | | || | | || |||| || | |||| ||| || | | |||| ||| | | | |||||
TGGTGAAATAGCTATTGGAACATCTCCTCAAAAGTTCACTGTCATTTTCGACACTGGCAGCTCTAATTTGTGGGTTCCATCATCTAAATGTACCTTCTCGgtgagtttttattttttaatttttttatatactaatctgttatttatg-acttgtgaatatgtatc-aatttaattccttatttattgcattttggttcag
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv10s0116g01210.t01 (Vitis vinifera), 5'ss of exon 2
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagca---acattt----ggactattgt----tgttagctgtggtt--------------gagatacttttgagtagaaaactaattgtgttctatctcttttgcag----------
|||||| || | ||||||||||| ||||| | ||||||||| | ||||||||||| ||||| ||||| ||||| |||||||| || ||||||||||| || ||| | |||| ||| | | |||||| || || | || || | | | | || ||| | ||| ||
TGGTGAAATTGGTATTGGTACTCCCCCTCAAACGTTCACTGTAATCTTTGACACTGGTAGCTCAAACCTGTGGGTTCCATCATCCAAGTGCTATTTCTCGgtgagcttccatatttctgtggaatgtgacaatatgttagtgaacatttttttttccatttcaagttggttggaagcaagagaatcatcatgtgtttgaattttgtcattttggtgcag
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ36863 (Selaginella moellendorffii), 5'ss of exon 1
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaacatttggactattgttgttagctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag
|| ||||||| |||||| | || || ||| ||||||||||| ||||||||||||| ||||| || |||||||| ||||| |||||| | | || ||||| |||| | | | | | | ||| |||
CGGCGAGATCGGCATTGGGAGCCCGCCGCAGGAGTTCACTGTGATTTTTGACACTGGTAGCTCGAATCTCTGGGTTCCATCGGGAAAATGTGTTCTGTCGgtaagt---atttccaggaattccacacgttttttcatggattcttgcag----------------------------------
upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ27796 (Selaginella moellendorffii), 5'ss of exon 1
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaacatttggactattgttgttagctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag
|| ||||||| |||||| | || || ||| ||||||||||| ||||||||||||| ||||| || |||||||| ||||| |||||| | | || ||||| | | | | ||| | | | ||| |||
CGGCGAGATCGGCATTGGGAGCCCGCCGCAGGAGTTCACTGTGATTTTTGACACTGGTAGCTCGAATCTCTGGGTTCCATCGGGAAAATGTGTTCTGTCGgtaagtattccaggaattccacacgtt--ttttcat--ggattcttgcag----------------------------------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|301502694|gb|HO208234.1|HO208234EST: ACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCA CTTGCATGTCTCTTGCATCCCAAATACAAGTCGTCTCGTTCAAGCACATAT
genomic: ACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaaca ... tcttttgcagCTTGCATGTCTCTTGCATCCCAAATACAAGTCGTCTCGTTCAAGCACATAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTGAGATCGCCATTGGTACTCCACCTCAGAAGTTCACTGTGGTTTTTGACACTGGGAGCTCTAACCTCTGGGTGCCATCATCAAAATGCTATTTCTCAgtaagcaacatttggactattgttgttagctgtggttgagatacttttgagtagaaaactaattgtgttctatctcttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT