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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa...

Basic information

species Arabidopsis thaliana
transcript AT1G49300.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g44050.1 (Oryza sativa), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa-----------
|||||| || |||||||||||||||||||| ||||| || ||||| || |||||| | || ||||| ||||| || || ||  |||| |||||||| || ||  | | |       ||||  |     ||   || |  |     | | ||| |  |  || | ||||   | ||  |||  || |  || ||| |  |            
ATATGTGAACAAGAAGTTCAGCAACCAGTACAAGGCTACGATTGGCGCGGATTTCCTCACCAAGGAGGTTCAGTTCGAGGATAGGCTCTTCACTTTGCAAgtaagatat-----ttcttttcccccgcactggttcttctcc---tcatcgc-gccgagattaattaggtccgttcatgg--gaagcgaatttgtatgagcttgattagtt

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G811797_T01 (Zea mays), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacct--cttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa--
|||||| || |||||||||||||||||||| ||||| || |||||||| |||||| | || ||||| || || || || ||| |||| |||||| | || ||  | | |||     |  || | |||  ||   |  | || |     |||    |||  | || |  |   ||      |    || |     |  | ||   
ATATGTGAACAAGAAGTTCAGCAACCAGTACAAGGCTACGATTGGGGCGGATTTCCTCACCAAGGAGGTGCAGTTCGAGGACAGGCTCTTCACTCTGCAAgtaagat-tggt--taccctagccgtatgccgtgccgtgatctgggagtagttatgtttctttacgccaacttcagccccgatt-agtactttcttaattagtt

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G04830.1 (Glycine max), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacc---tcttttattttattttagcgc--agttggtataagttagactccttagtggcagaggaaaacttggaataa
 ||||| ||||||||||| || || ||||| |||||||| ||||| || ||||| || || || ||||| |||||||||||  |||||||||| ||||||||||||    |||| ||||    ||     |   || | | | |||| ||| | |  | || |    ||    | |  || ||  |  |  ||        |   
GTATGTGAATAAGAAGTTTAGTAATCAGTACAAGGCAACCATTGGAGCGGATTTTTTAACCAAAGAAGTGCAATTTGAAGATAGGCTTTTCACCTTACAGgtttgtga--gcagtgcttacctagattttcctatcgtatgtgttatgttacccctaattttgctggagaattattggtttgtaacctactaacctccttta---

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G12630.3 (Glycine max), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttag--actccttagtggcagaggaaaacttggaataa
|||||| ||||||||||| || || ||||| |||||||| ||||| || ||||| || || || ||||| ||||| |||||  |||||||||| |||||||||| |||  |||| ||||    ||     |   | |  | |  | |    |   || | | | | |   | |  |  || |   | |   | || | || |
ATATGTGAATAAGAAGTTTAGTAATCAGTACAAGGCAACCATTGGAGCGGATTTTTTAACCAAAGAAGTGCAATTCGAAGATAGGCTTTTCACCTTACAGgttt-ttg-agcagtgcttacctagattttcctatcttatgtgctatgttactactgattttactgaagaattattgggttgtgcatgttgattttgcatga

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv03s0063g02420.t01 (Vitis vinifera), 5'ss of exon 4
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgc-tttatcagtaaacctcttttattttat---tttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa
|||||| ||||||||||| ||||| || || ||||||||||| || |||||||| ||||| |||||||| || || |||||  |||| ||||||||||||||| ||  |      |  ||| |   | |||       |  || |    |||  | |   ||     ||  |   |   | | |  | |    | |||| |   
ATATGTGAATAAGAAGTTTAGCAATCAATACAAGGCAACTATCGGAGCTGATTTTTTGACGAAGGAAGTGCAGTTCGAAGATAGGCTCTTCACTTTACAGgttagtgataattttgagtttcttgctcaactggcaaaaacttgtaagcttattgtatgcgg-gggcgtgtgttccaaaattcgatgtgcttgatttggca---

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 2
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa---
 |||||||| |||||||||||||||||||||||||| || ||||| || ||||| ||||| || ||||| ||| | |||||| ||||| ||||  | |||||  ||  |  | | |   |     |  || |  |||  |  || || || ||||  |  |   |   |  || |        ||    |  || | | |   
GTATGTTAACAAGAAGTTCAGCAACCAGTATAAGGCCACGATTGGAGCAGATTTTTTGACAAAAGAAGTGCAAGTCGAAGACAGGCTTGTCACAATGCAGgtcagtaatctctgtg---tgctgatctacattcttttctgaatgttggcccagtgtgacttgttcccatcccctgagccggtagactgatatgaattcatgg

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S61_279V6.1 (Physcomitrella patens), 5'ss of exon 2
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcag--ttggtataagttagact--ccttagtggca-gaggaaaacttggaataa
 |||||||||||||| |||||||| || |||||||| ||||||||||| || ||  | ||||||||||| ||  |||||||| | ||| | ||  | |||||| ||     |     ||    |    | | |   |   |  || |||    |   || |  |   |  | |  |   |||   | |  |||  ||   |    
GTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAGGTTGAAGACAGACTTGTTACGATGCAGgttagtctcctcctt-tttcgcaaacggagcccagatgactgcttgtagtatggaactgattgagcatctattggctccagttagatggagaaggctctca----

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S119_112V6.1 (Physcomitrella patens), 5'ss of exon 2
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa---
||||||||| |||||||| ||||||||||||||||| || ||||| || || || ||||| || || || ||| | |||||| | ||| | ||  | |||||  ||     | ||     || | |    ||    ||  ||  |||  |  ||||| | ||   |  |   |||     |   |      |||||  ||   
ATATGTTAACAAGAAGTTTAGCAACCAGTATAAGGCCACGATTGGAGCAGACTTTTTGACAAAAGAGGTGCAAGTCGAAGACAGACTTGTGACAATGCAGgtccgtaactcccgcatacgatgact--gtcttaagtacgttggtttt-caaagttgatgtagtgtgaatggcttccattctctgtgctggttggatgaattg

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S61_292V6.2 (Physcomitrella patens), 5'ss of exon 2
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa---
|||||||||||| ||||||||||| ||  | ||||| |||||||| ||||||||| | ||||| |||||  || |||||||| | ||| | ||  | |||||  ||  |  |||||  | ||  |      |   || | || |   |  | |    || | |   |  |    | ||   |  |  | ||| |     |   
ATATGTTAATAACAAGTTCAGCAATCAACACAAGGCCACTATTGGAGCTGATTTCCTAACTAAAGAAGTATAAGTTGAAGACAGACTTGTTACAATGCAGgtcagtgattccagcgtgtgat-ggctcgtgtgagttgtcttctcaaattggatccagtgtga--catgcattatcgtttgaatgtgagactggagtcgagtt

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ15497 (Selaginella moellendorffii), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtgg-cagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa
|||||| ||||||||||| ||||||||||| ||||| |||||||| || |||||  | || ||||| |||||| | || ||| ||||  | ||  | |||||  || |||  |   |||  |  |  |||  |||||  | |||         | |||| ||   || |  |    ||                       
ATATGTGAATAAGAAGTTTAGCAACCAGTACAAGGCTACTATTGGAGCCGATTTTCTCACCAAGGAGGTTCAAGTGGAGGACAGGCTAGTGACGATGCAGgtgggtcgtgatctttgctcca--aaaaaatttctttcttcttacg-------aattgggat---tttggttttccag-----------------------

upper sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ24755 (Selaginella moellendorffii), 5'ss of exon 3
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa
|||||| ||||||||||| ||||||||||| ||||| |||||||| || |||||  | || |||||||||||| | || ||| ||||  | ||  | |||||  || |||      ||||      |||    || | | || || |  || | |||| ||   || |  |    ||                       
ATATGTGAATAAGAAGTTTAGCAACCAGTACAAGGCTACTATTGGAGCCGATTTTCTCACCAAGGAAGTTCAAGTGGAGGACAGGCTAGTGACGATGCAGgtgggtcgtgat----ctttgctccaaaaaaaattctttcttcttcttacg-aattgggat---tttggttttccag-----------------------

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|125022529|gb|EL094798.1|EL094798
EST:     ATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAG                         ATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTG
genomic: ATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtg ... ttttttacagATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTG
EST: gi|125276016|gb|EL290101.1|EL290101
EST:     CCGGCTTTTCACTTTACAG                         ATCTGGGACACAGTTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTGCGTTT
genomic: CCGGCTTTTCACTTTACAGgtttgttgtg ... ttttttacagATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTGCGTTT
EST: gi|19874664|gb|AU235495.1|AU235495
EST:     ATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAG                         ATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTGCGTTT
genomic: ATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtg ... ttttttacagATCTGGGACACAGCTGGTCAAGAAAGGTTTCAGAGTCTTGGTGTTGCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAGgtttgttgtggcagcgctttatcagtaaacctcttttattttattttagcgcagttggtataagttagactccttagtggcagaggaaaacttggaataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA