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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG

Basic information

species Arabidopsis thaliana
transcript AT5G18420.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatg--cttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
||| ||| ||| | | | | || || | | | || | | || | | | | | | | ||| ||||| || | || | ||| | ||||||| ||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || | || || | |
gtatgtctgtttcttttctttgctagtcaatatgatcaccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
-----------------gtaagtcatcaccttattggttccaccatttactt-tcgaccaaaattata-acttttaaagtgggaatc-taagaatgcttctt---cagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| | || || || | | ||||| | || | || | ||| || || | || | | | ||||| ||| || | ||| ||| | | ||||| |||||||| || |||||||||||||| || |||||||| || ||||| || || || | ||||| |
gtatgtagattagccttgtcgtttattctattgttttcttatttaattactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G133757_T01 (Zea mays), 3'ss of exon 9
----gtaagtca-tcaccttattggttccaccatt-tactttcgaccaaaattataactttta-aagtgggaatctaagaatgcttctt-------cagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| | | | || ||| | | || | ||| | | | | || | | | || | | ||| | | ||| || | ||| ||| | | ||||||| |||||| |||| ||||||||||| || || |||||||| |||||||| | | || | || | |
gtacacatactagccttttcatctgttttatctttatccttgtaattattgtgcttttttctgcatgccagatttcacacttgccttattgttcaacagATACTTTGATGCTATTGTCCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAACAGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAC

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G011575_T02 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------gtaagtcatcaccttattggttccaccattt------actttcgaccaaaattataacttttaaagtgggaatctaaga-atgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| ||| | ||| | | || |||| | | | | | || | | | | | | | | || ||| ||| || | ||| ||| | | ||||||| |||||| |||| ||||||||||| || ||| ||||||| |||||||| | | || | || | |
gtatgcatacttagccttttcatttgttttatctttatccttgtaattattgtgcttttttctctttgagacaaaggtcgggagctttcaattccgactattttaaaaaattattgtgcttttttctgcatgtcatatttcacacttgccttattgttcgacagGTACTTTGATGCTATTGTTCATATGGATATGAGCTTGCATTCAATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCAT

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 9
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttc-----agCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| ||| | | |||||||| | || | || | ||| | | | ||| | ||| || || | ||| | ||| | | ||||| |||||| |||| || |||||||||||||| || ||||| ||||| ||||| ||||| | || || | |
gtgtgtctctgctct--tggttccatgttctattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 9
----------gtaagtcatcaccttattggt--tccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttc--ttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| || | |||| || | | | ||| || | | ||| | ||| | || | || | | ||| || | || || | |||||||||||||| || || ||||||||||||||||| ||||| ||||| ||||||||||| || | ||||| |
gtatgcatttttcctctattatattatctgtgctttagtacatacattgccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTCACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTTACAACAGCAGTTGAACTACCGTCTCAATTCATTCAC

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
----------gtaagtcatcaccttattggt--tccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttc--ttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| || | |||| || || | | ||| || | | ||| | ||| | || | || | | ||| || | | || || | |||||||||||||| || || ||||||||||||||||| ||||| ||||| || |||||||| || | ||||| |
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
|| | || | | | | | || | |||| || | |||| | ||| || || || || | || ||| | | ||||||||||||||| || ||||||||||| || || ||||| || || || ||||||||||||| || || |||
gtatgtttttgtcatgttgatttacctttcttgctttattactgaaatgataagcatcccagcactttaatct-ttttcttttttttttctgtatttttgctttcctttcttttt-tgtcaatttagGTACTTCAGAGTTCTTGTCAGTATGGACATGAGCCTACATTCAATGGAAGTCGTTAACAGGCTTACTACAGCGGTTGAACTTCCCACCGAATTTGTACAC

upper sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ16277 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
| ||| | | | |||| || | | | | || | |||| ||| |||| | || || | || |||||||||||||||||||| |||||||| || ||| | || ||||| || || | | || || | || |
-------------------------gtaagtacgtctg-tggagattacaagctgtttatctcgcttcg------gtttctacagGTATTTCAACGCGCTTGTAAGCATGGACATGAGCCTGCACTCCATGGAAGTCGTCAATCGCCTGACAACGGCCGTGCAGATCCCTGTCGAATATATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG
               ttataac  putative branch site (score: 2)
 tgcttcttc  putative PPT
 aaaattataactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG