Sequence
atgc intronic sequence ATGC exonic sequenceCTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttcttttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35950.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttcttttacag-------------------------------
|| |||||| | ||||| ||||||| ||||| |||||||||||| |||| |||||||| || || || ||||| || |||||||||||||| ||||||| || | | | | || || || ||| || | | |||| | ||||||| | | |
TTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGTTTCAAAGAAGgcaagggac--tcactttcattttctgtt-aataatattgatgtgctcttttt--ttcttctttcgctaaagaagtttgttggtcatgtttaatttgagatcgtc
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttc--gtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttctt-------ttcttttacag-------------------
|| |||||| | ||||| |||| || ||||| ||||||||||| |||| || ||||| || || |||||||| || |||||||||||||| ||||||| || || | | | | || | ||||| | ||| | ||| | | | | | ||| ||
TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctctgattcttattt-tctattatttggct-ttgtgttttctttagtccagcgtcctctggaaatgcttgtttttagctcatttaccttacagtct
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcag--------tttcgtccgaactggtcgactat-ttaacaattgagagttccaaattttgatgcttctt-----ttcttttacag------------
|| |||||| | ||||| |||| || ||||| ||||||||||| |||| || ||||| || || ||||| || || |||||||||||||| ||||||| || | | || | | | | | || || | | | | |||| | || | | | | || ||
TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAAGCCAGCTATGAGAATGTTTCGAAGAAGgcaagacactgattcttgtattctatatttggttttgttcactctacatgttactttatttcggtgttctctgggcatcttgttttagttcatttaccag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttcttttacag---------------------------------------------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| ||||||||||| || || ||||||||||| || ||||| |||||||| ||||| || || ||||| ||||| || | | | || || | | || | || | || ||| |
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgt--acttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G05160.1 (Glycine max), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagtt--ccaaattttga-tgcttcttttctt-ttacag----------------------------------------------------------------------------------------------------
||||| |||||| ||||||||||||| |||||||||||||||||||| | || ||||||||||| || ||||| |||||||| ||||||||||||||||| || ||| | ||| | ||||| || ||| ||||||| || ||| | | | | ||||
TTATAATAGATTACGACCTTTGAGTTATCGTGGTGCTGATGTTTTCATATTAGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTTTCCAAGAAGgt--actttttccactatagtccaaagtttaagttcctagtgttgctcaaatttagaatgcacttctacatgttacctttaatgtaaatgtgatgtttccataataattgtaaagaactatatcctatttatattaattaaaaagtgctaataaattgtgtgttattttcattttcag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G23340.1 (Glycine max), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttctt-ttacag--------------------------------------------------------------------------------------------------------
||||| |||||| ||||||||||||| |||||||| ||||||||||| | || |||||||| ||||| ||||| |||||||| ||||||||||||||||| |||| | | | | ||| | | | | | || || || |||| ||| | |||||
TTATAATAGATTACGACCTTTGAGTTATCGTGGTGCCGATGTTTTCATATTAGCTTTCTCTCTGATTAGCAAGGCCAGTTATGAAAATGTTTCCAAGAAGgtacttttcccactatttcaaggtttatgttcctagt-attcctcaaatttaaaatgcacttttacaggttacattcgatgtaaatgtaatgtttccataacaattgtaaagaaccatatcttatttatattaatttaaaagtgttaataaacggtgtatgtgttattttcactttcag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 4
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaatt---gagagttccaaatt---ttgatgcttct---tttcttttacag--------------------------------------------------------------------------------------------------
|| |||||||||||||||||||||||||||||||| ||||||||||| | || ||||||||||| || ||||| |||||||| ||||| || || ||||| ||||| || | | | | || |||| ||| | || |||| | | || | || |
TTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgt--acttcgttgcaatttattgtggtcagagtgttttgggagaattcttatttcttttgagaatcatgaggtttctgtatggcctgtaacgaaggatgtatggatcatgttatattttaagaaaataattcatttatataaaaagtcgatgataaattgcatgtctggtttctttttcag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcag--tttcgtc--------cgaactggtcg-actatttaacaattga--gagttccaaattttgatgct--tcttttcttttacag--------------------------------
|| |||||||| |||||||||||||| || || || ||||||||||| | || ||||||||||| || ||||| || ||||| ||||||||||||||||| || || | ||| || | | ||| |||| | | | || | |||| ||| |||| | | || | | |
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 5'ss of exon 3
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgact---atttaacaattgagagttccaaattttgatgcttcttttctt-ttacag-----------------------------------------
|||||||| | ||||| |||||||| | |||||||||||||| | || || |||||||| || || || |||||||||||||| | || |||||||| | || | | || | || |||| | || | | | || || || | |
TTATAACAGGCTTCGACCTCTGAGTTACAGGGGTGCTGATGTTTTTCTACTAGCATTCTCTCTTATCAGCAAAGCTAGTTATGAGAACATCTCAAAGAAGgtactagccctctgcatcagtggcctcacatttgtgtcctaaggagtagatgcgcgaccgtttggttgattgctgtactcggtggattgcattgattctgacgatttattacatggcagMapped 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|164012034|gb|ES176193.1|ES176193EST: TTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAG TGGATTCCTGAG
genomic: TTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcg ... tcttttacagTGGATTCCTGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttcttttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG