Sequence
atgc intronic sequence ATGC exonic sequenceGATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35230.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os10g39670.1 (Oryza sativa), 5'ss of exon 4
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
||||||||||| ||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||||| | || |||||||| || |||||||| |||||||||| | || || || | | | | | || |||| | | || || | ||| ||| | |||| | | || || | |
GATCCTCGTCTATCATGCTTTGGTTTGATGAAAAACAGCAGGGATGGGAAAAGTTATAGTACAAACCTGGCATATACACCTCCAGAATATCTGAGAAATGgtacttgatttttcacattct-tgcttaccagtcttgaa--aacaaattatccagtattctcttttcggcagt----tctcttcacttatctgggggaaccattttt------------------
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 5'ss of exon 4
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
||||||||||| ||||| |||||| ||||||| ||||| |||||||| ||||||||||||||||| | || |||||||| || || ||| | |||||||||| | | | || | | | ||| | | | | | || | || || || | |||| | | ||| | ||
GATCCTCGTCTTTCATGCTTTGGCCTGATGAAAAACAGCAGGGATGGCAAAAGTTATAGCACAAACCTTGCATATACACCTCCAGAGTATTTGAGAAATGgtacatatgccttttaccctgagactaaaaactattcttttcctctgagatatgaactgctatttattaaagagaaaatccaagaaatgatattgacaag-------------------------
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G099598_T01 (Zea mays), 5'ss of exon 4
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagca--acttgtttatactcta--tagatt-------attatacaatcaacata---aaactcaaatttata-gtttttgcactgaaacttcttgaagcaaagatgg-----atctcagtg-tgataaattttgtgttgcag---------------
|||||||| || ||||| |||||| ||||||| |||||||||||||| ||||| |||||||||||| | || |||||||| || |||||| ||||||||||||| | | |||| ||| | ||| | ||| | | ||| || | | | || | | | || || | || |||| | |||| || | || |||| ||| | |||
GATCCTCGCCTTTCATGCTTTGGCCTGATGAAAAACAGTAGGGATGGGAAAAGCTATAGCACAAATCTTGCATATACACCTCCAGAATATTTAAGAAATGgtaacatatgatttgtctatgacaaacttagccttctttgaattgtttagtcagggtatttagaagtgggtatacatgacagtaca-tgctatttactgaaaatagaatggctaacattttcgtaatgatgggatttccatggcaacctatgctgcttcag
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G127050_T02 (Zea mays), 5'ss of exon 4
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgta--aagcaacttgtttatactcta--tagatt-------attatacaatcaacata--aaactcaaatttata-gtttttgcactgaaacttcttgaagcaaagatggatctcagt------gtgataaattttgtgttgcag----------------
||||||||||| ||||| |||||| ||||||| ||||| |||||||| ||||| ||||||||||| | || |||||||| || |||||| | |||||||||| | | | || | ||| | ||| | ||| | | | | || | | || || | | || || || | || |||| | |||| | || | |||| ||| | |||
GATCCTCGTCTTTCATGCTTTGGCCTGATGAAAAACAGCAGGGATGGGAAAAGCTATAGCACAAACCTTGCATATACACCTCCAGAATATTTGAGAAATGgtagcatacgatttatctatgacaaacttagccttctttgaattgtttagttagggtatttagccgtgatatacatgacattaca-tgctatttactgaaaatagaatggctaacattttcctaatgatgggatttccatggcaacctatgctttcttcag
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G00540.1 (Glycine max), 5'ss of exon 2
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatca-acataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
||||| |||||||| || ||||| || ||||||||||| ||||||||||| ||||||||||| ||| | ||||| ||||| ||||||||| ||||||||||||| ||||| || ||| | | || || ||| | | || ||| ||| || | || | | | |||||
GATCCCCGTCTCTCTTGCTTTGGTTTTATGAAGAACAGCAGGGATGGTAAGAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAATGgtaac-caactccctt---ctcgacattttcttttacttttttatgtataacg-------ataattctctcaatcagatttcttttttttccag--------------------------------
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G48030.1 (Glycine max), 5'ss of exon 2
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
|||||||||||||| || ||||| || ||||||||||| |||||||| || ||||||||||| ||| | ||||| ||||| ||||||||| ||||||| ||||| |||| || | | | || ||||| | || |||| | | | | | | | ||| | ||| ||
GATCCTCGTCTCTCTTGCTTTGGTTTTATGAAGAACAGCAGGGATGGCAAGAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAACGgtaac-taactcccttctcgacatttactttttatata--taatataata-----actcgtttctctcaatcggaatgcttttgttacag-----------------------------------
upper sequence: AT4G35230.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 5'ss of exon 4
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
|| || || || |||||||||||||||||||| || ||||| ||||| |||||||||||||||||| | || || ||||| || ||||||||||||||||||| | || | | | ||| ||| | | |||| || | | || ||| | | | || | ||| | |||| | | ||| || | | |
GACCCACGGCTTTCATGTTTTGGCTTGATGAAAAATAGTAGAGATGGGAAAAGTTATAGCACAAATCTTGCCTACACACCTCCGGAATATCTAAGAAATGgtacttct-ctaatctgaatgatatctatttgtttg---tcaa-atgtcatttaagttttccggtacttca-taaaatgttgtgaaactgatctggctccccttat-------------------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|124979817|gb|EL052816.1|EL052816EST: TACACCACCTGAATATCTAAGAAATG GAAGAGTGACACCTGAAAGTGTTACGTATAGCTTTGGAACTGTCCTTCTGG
genomic: TACACCACCTGAATATCTAAGAAATGgtaaagcaac ... tgtgttgcagGAAGAGTGACACCTGAAAGTGTTACGTATAGCTTTGGAACTGTCCTTCTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATCCTCGTCTCTCATGTTTTGGCTTGATGAAGAACAGTAGGGATGGTAAAAGTTATAGCACAAATTTAGCTTATACACCACCTGAATATCTAAGAAATGgtaaagcaacttgtttatactctatagattattatacaatcaacataaaactcaaatttatagtttttgcactgaaacttcttgaagcaaagatggatctcagtgtgataaattttgtgttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA