Sequence
atgc intronic sequence ATGC exonic sequenceCTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54230.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G18030.1 (Glycine max), 5'ss of exon 1
CTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacag
||||||||| |||| |||| || || |||| |||||||||||||| ||||||||||||| ||||||| ||| || ||| || |||| | | || | | ||| | | | || | || |
----------------------------------------------------ATGGATCCTGGTCGCTATGCTCTGCATCAAGGCTGGGATAATAACAGCgtaattgtggtttcctccttaaata-attcacctatatggaatatatggggatcattattcaaagaaactact-actattagggtttcaatctcattgattt----------------------------------------------------------------------------------
upper sequence: AT3G54230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 1
CTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacag
||||||||| |||| |||| || || |||| |||||||||||||| ||||||||||||| ||||||| ||| || ||| || |||| || |||| | |||| | | | || | || || ||| | |
----------------------------------------------------ATGGATCCTGGTCGCTATGCTCTGCATCAAGGCTGGGATAATAACAGCgtaattgtggtttcctccttaaata-attcacctatatggaatatatg---gggatcattattcaaagaaact-actattagggtttcaatct-----gattgatttttt--------------------------------------------------------------------------
upper sequence: AT3G54230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 5'ss of exon 1
CTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctcctta----catatatgggatgataa-acaagatatt------tttagggatgt----tatgaatctcaactcatccgtg--------gagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgat-gtttgttgctgacatagcttattctcttcaattcacag
||||| ||||||||||| |||| ||||||| ||||||| ||||||||||||||| ||||||||||||| ||||||| | ||||||||||||||| |||||| ||| || | ||| | | || || ||||||| | ||| || || | |||| | ||||||| |||| ||||||| ||| | || | ||||| ||||||||||||||||||||||||||| ||| |||||
-----------------------------------------TCTGGCAAGAAATGGATCCAGGTCGCTATGGTCTCCAGCAAGGATGGGATAATAACAGCGTAATTGTGgtttcctccttaatcacctatatgggatgataatacaagaaattagggctcttctgattgtccattttttatggcatctcatccttaagaacaatgagagaaagccgtggggcattgaggatatggaatggatttgccta-cctcgtacc-----atgattatttgttgctgacatagcttattctcttgaatccacag
upper sequence: AT3G54230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 5'ss of exon 1
CTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctcctta----catatatgggatgataa-acaagatatt------tttagggatgt----tatgaatctcaactcatccgtg--------gagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgat-gtttgttgctgacatagcttattctcttcaattcacag
||||| ||||||||||| |||| ||||||| ||||||| ||||||||||||||| ||||||||||||| ||||||| | ||||||||||||||| |||||| ||| || | ||| | | || || ||||||| | ||| || || | |||| | ||||||| |||| ||||||| ||| | || | ||||| ||||||||||||||||||||||||||| ||| |||||
-----------------------------------------TCTGGCAAGAAATGGATCCAGGTCGCTATGGTCTCCAGCAAGGATGGGATAATAACAGCGTAATTGTGgtttcctccttaatcacctatatgggatgataatacaagaaattagggctcttctgattgtccattttttatggcatctcatccttaagaacaatgagagaaagccgtggggcattgaggatatggaatggatttgccta-cctcgtacc-----atgattatttgttgctgacatagcttattctcttgaatccacagMapped 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|125299566|gb|EL313651.1|EL313651EST: TGGTCGTCAGCAAGAATGGGATAATAACAGT GCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
genomic: TGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtgg ... caattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTTGAATATTCTCTCAGACCATCAAAGATTTGCTTGGTGCACTGGCCGGAAATGGATCCTAGTCGATATGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA