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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

Basic information

species Arabidopsis thaliana
transcript AT4G29040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4
gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
| |||||| | | ||| | || ||| || ||||| | ||| | || | | || || | | |||||||||||| |||||||| | | || ||||| ||||| ||||||||||||||||| || || ||||| || || ||||| || || || ||||| |
-----gtgcttttctac-aatgtttcaagttc-tgtcttattggaaacctgcttcgttcttatca--atagtttttgggtgca-----gATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 3
gtaatatataattctactgagatggcaaat-caatgact-tgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
||| | | | ||| | | || | || ||||| || ||| | || | | |||| | | |||||||||||||||| ||||| | | || ||||| ||| | ||||||||||| ||||| ||||||||||| || || |||||||| ||||| || ||||
gtactgtgacgtctgtaaatgataatatttgcattaacaatgttcttaataccctttgttcttattatagaaggttgtaaacttgtg-cagATACACACATCGAAAATGACATTAGCTGATGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
gtaatatataattctactgagatggcaaat-caatgacttgttcg-------aaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
| ||||| || |||| | | | | | ||||| ||| | || ||| || ||| | |||||||||||||||| ||||| || | || ||||||||||| ||||||||| | ||| | ||||| ||||| ||||| ||||| || ||||| || || |
-------gtgcttcta-tgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
-----gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
|||| || | | | | || || | | | | || || |||| | | | || ||| | |||| |||||||| || ||||| | | || ||||| ||| | ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||
gtgctgtaacatctgtagacagtaatatt-tgcattatcaatgttcgtaatacctttttgtcctt----ataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 4
---gtaatatataattctactgagatggcaaatcaatgacttgtt----cgaaactttcttgttcattgaggttgtgggttct----gtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
|| ||| || | | | | ||| | || || ||||| || | | || ||||| ||| || |||||||||| || | |||||| | | || ||||| ||| | ||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| |
aacccaagatacgatgttgtttctgctgattctatgtgatatcttaacatgatactttgttcaatcatatgcttaaatgttctcatactttggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGACGAATTCTCCGGAGCTGATATAAAGGCAATATGTA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4
-------gtaatatataatt-ctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttct----gtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
||| || | || || |||| | | | | || | |||| | || | |||| ||| || ||||||||||||||| |||||| | | || ||||| ||| | ||||| ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| |
acccaacataagatgttgtttctgctgattctatgtgatatcttaacatgcatactttgttcaatcat-atgcttatacattctcatactttggaattaagATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gtaatat-----ataattcta-ctgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggtt--gtgggttctgtttataaaa----tagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
| ||||| ||| || | | || | ||| | | || || |||| | | | | | | ||||| || ||||||| ||||| | |||||| | | || ||||| ||| | ||||| ||||| ||||| || || ||||| || ||||||||||||||||| |||||||
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gtaatatataattctactgagatggcaaatcaatga-cttgtt---cgaaactttcttgttcattgaggttgtgggttctgtttataaaat----agATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
| | | || | | || ||| | | | | |||| | ||||| | | ||| || | ||| ||| |||| || || | | |||| || || || | |||||| | | || ||||||||||| || |||||||||||||| ||||| ||||| || || ||||| || || ||||| || |
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgctt--gttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
|| | | | | | | ||| || ||| | | ||| | || |||| || ||||||| ||||| ||||| || ||||| ||| | |||||||||||||||||||| ||||| || || |||||||| || ||||| || ||||
---------------------gtgacgtgttttttttctttgtgcgcgtttgtttttcctaaccactttggttcttgc---------agATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 4
gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
| || | | || |||| || | | || || | || |||||| |||| || ||||||| ||||| ||||| || ||||| ||| | |||||||||||||||||||| || || ||||| |||||||| || ||||| || ||||
------------------gtgacgtcgtgcttattttttgtgcgcgtttgtttttcccaaccacttt---ggttctt--------gcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGATGAATTCTCTGGAGCTGACATCAAGGCAATGTGCA

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|86082474|gb|DR378233.1|DR378233
EST:     AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
EST: gi|125048107|gb|EL120376.1|EL120376
EST:     AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGG
genomic: AAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGG
EST: gi|124706458|gb|EH797860.1|EH797860
EST:     ATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: ATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
EST: gi|125060037|gb|EL128714.1|EL128714
EST:     CGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAG                         ATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT
genomic: CGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgtaatatata ... tataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA
                                      ttctgttt  CT-rich tract
 ttctgtttataaaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT