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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttgtagacccttatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataaatgctgtt...

Basic information

species Arabidopsis thaliana
transcript AT5G58060.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 5'ss of exon 4
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttgtagacccttatacataagcggtacttccttttctaagtttcagta-tacttgc-caattatacataa--atgctgtt
||||| ||||||||||| ||| |  |||||||||||||||| |||||||| ||||| |||||||| ||||||  |   | |    |        | |   |   | |     |  | |    ||  ||| |  ||  | | ||||  | |  | ||  ||  |  |  | 
GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtatttcttac----cagaaaaaaaaattatagaatagctctgccattcatattggtaaataccaacacttcttgttctaacaaactcaatgacccgatc

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 5'ss of exon 4
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttg-tagacccttatacataagcggtacttccttttctaagtttcagtatacttgcca-attatacataaatgc-tgtt
|| || ||||||||||| ||| || ||||||| |||||||| |||||||| || |||||||| |||||||||        || || |   ||  || | ||| ||    ||    |||    |  |   | |  ||   | |||     | | | |||  || | ||  
GATCCTGCAGAGGCTGACAAGTTGCTGAAAATTCAGAGGGATTTGGATGAAACTAAGATTATTCTTgtaagtaactctatcgctcatgaattaatatatcctgat-tgcaatttataccctatgctggcaatggcatattccttatttcagtgtgcatggattcatg--

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 4
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttgtagacccttatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataa----atgctgtt
|| || ||||||||||| ||| || ||||||| ||||| ||||||||||| ||||| || |||||||||||       | |  |   |  ||| | | |  ||||      |  | | || ||| |    | | |   |||||  |    | ||||      |||  |||
GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgcaatac--tttatatttgcaaaacagtatatgggttcccttcatcttttacct--tctaaagttacttctcttcaagacattctgtcatgtagtt

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G13840.1 (Glycine max), 5'ss of exon 4
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttgtagacccttatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataa-atgctgtt---
|| || |||||||| || ||| || ||||||||||||| ||||||||||| || || || |||||||||||  |    | |  | | |  ||| | | |  ||||      |  | | || |||      | | |   |||||  |  | | ||||    |||  |    
GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacacaatac--ttcatatttgcaaaacagtatatgggttcccttcatcttttgtct--tctaaagttacttctctttaagacattctgtgccatgtag

upper sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctc-------cggtcctttct---tgtagaccct-tatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataaatgctgtt
|| || || |||||||||||| |||||||||| ||||| ||||||||||| || || ||||| ||||| |||  |   |        |  |  ||| |   | |||| ||  |||| ||||   |    || || |||    |||       ||  || ||  | |||  ||     
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttc------tttatcagtt-catatacctgt----

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|86082551|gb|DR378310.1|DR378310
EST:     ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTCTAGCCCGTGGTGANAAGCTGGACAGCCTA
genomic: ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
EST: gi|125121703|gb|EL168741.1|EL168741
EST:     ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTCTAGCC
genomic: ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCC
EST: gi|125249409|gb|EL263494.1|EL263494
EST:     GTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
genomic: GTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
EST: gi|116387908|gb|EG430500.1|EG430500
EST:     ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTTTAGCCCGTGGTGAGAAGCTGGACAGCCTA
genomic: ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
EST: gi|164126787|gb|ES164832.1|ES164832
EST:     AAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
genomic: AAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCCCGTGGTGAGAAGCTGGACAGCCTA
EST: gi|125308143|gb|EL322228.1|EL322228
EST:     ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTT                         CATAAAACCATTGATAGTGTTCTAGCCCGTGGTG
genomic: ATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctg ... tgtattgtagCATAAAACCATTGATAGTGTTCTAGCCCGTGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctccggtcctttcttgtagacccttatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataaatgctgtt

- - - - - - - - - AAGCTG
- - - - - - - - - - GCTGTT