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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaatccttttctatggctctttttctctgtgatgcttgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G26360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------------gtaaattaatcct--tttctatggctctttttctctgtgatgcttgttgcttctctcctctggtttcagatcatcgttgtttttgtggt-acagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
                                                                     ||  | ||||     |    |||   |    |  |  || |         || | |    |   || |    | | ||   | |||  |  |||||||| || |||||||| || ||||||||||| ||||  || |||||||||||||||||||||||||  ||||
gtacaactggtcacctctttaggcttcatgtagttaactccatgttgtgtttgatgtcattgacaggttgttgagtaataagaatgatgatgtaaccggcttcccatgtttgagcccatttttttttaattacttgatgataccattcgatctgtttttgcagGCTGTGGCGGATATCATACGCACAACATTGGGCCCTCAGTCAATGTTGAAGATGCTTCTTGATGCTGCAGGAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 2
---------gtaaattaatccttttctatggctctttttctctgtgatgcttgttgcttctctcctctggtttcagatcatcgttgttt-ttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
         |    |    |    | ||    |  ||   | || ||       ||  | | |||| |   ||   |  | |||  |   |||   | |||||||| || || ||||| ||||| ||| | |||||||| || ||||||||||||||||| ||||||  |||||
gacctagctggctgtctggctagctgtaaaaattgttaattttgagaacagaaatgaattt-tcctgtcacttggtaaaaccgtgatcaattgctctgcagGCTGTGGCAGACATCATCCGTACTACACTCGGTCCTCGGTCCATGTTGAAGATGCTTCTGGATGCTTCTGGAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 2
----------gtaaattaatccttttctatggctctttttctctgtgatgct-tgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
          | |||||  || |  |  | ||||    ||  | ||    || |  | |||| ||  ||   |   |   |||  |  | |||     ||||||||||||||| |||||||| || |||||||||||  | || ||| |||| |||||||| || ||||||||||
ctcatgttgtgcaaattggtcttgatgaa-ggctacagttagccgtttgactgtactacttcactgttc-aataatattccatgttaatattttcttcacagGCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------------gtaaattaatccttttctatggct------ctttttctctgtgatgcttgttgcttctctcctctggtttcagatcatcgt------tgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
                                                                                                  | ||  | |  | | ||   |||       || || |   ||| |  ||  | ||  ||   |||  || |      | |      |  | || |   ||||||||| ||||| ||||| || || |||||||||||  | || ||| |||| |||||||| |||||| ||||||
gtacagattctcaagctgctccgctcgttcgctttagtggcctctaagaatgtagtccgattaattcagtgttactgtggaacagtacaatttgtagttgaaccatttgtctgctcatgctgtgcaaattatttttgatgaaggctgcagtttgactgtactgtatttaacattccatgttaaataatattttatcacagGCTGTCGCTGACATCATACGCACTACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGATGCTAGTGGAG

upper sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaaattaatcct-tttctatggctctttttctctgtgatgct-tgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
         || | |   | || |||  ||   |   ||    ||||    | || |||| |  |   ||  | |   | |||  ||     ||    ||||||||||||||| || || ||||| || |||||||| || || |||||||||||||| ||||||||||||||||
actgataaagttactaggttctgtttgaatatgtaggttggcatgtgcaattgtgctgct-caatgaactaatgttgca-catttttacaaatgcttgacagGCTGTTGCTGACATAATACGTACTACCTTGGGTCCACGATCCATGTTGAAGATGCTACTTGATGCTGGTGGAG

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|124822535|gb|EH907401.1|EH907401
EST:     TAAGGTTCATCATGGTAATATCCAAGCTTCCAAG                         GCTGTTGCTGATATCATTCGTACAACATTGGGTCCTACGTTCTATGTTGAA
genomic: TAAGGTTCATCATGGTAATATCCAAGCTTCCAAGgtaaattaat ... tgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCT-CGTTCTATGTTGAA
EST: gi|47829135|gb|CK118819.1|CK118819
EST:     AGCGTGAATCTGGAAGTAAGGTTCATCATGGTAATATCCAAGCTTCCAAG                         GCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
genomic: AGCGTGAATCTGGAAGTAAGGTTCATCATGGTAATATCCAAGCTTCCAAGgtaaattaat ... tgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
EST: gi|86074170|gb|DR369927.1|DR369927
EST:     AGCGTGAATCTGGAAGCAAGGTTCATCATGGTAATATCCAAGCTTCCAAG                         GCTGTTG-TGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
genomic: AGCGTGAATCTGGAAGTAAGGTTCATCATGGTAATATCCAAGCTTCCAAGgtaaattaat ... tgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
EST: gi|47830309|gb|CK119993.1|CK119993
EST:     AGCGTGAATCTGGAAGTAAGGTTCATCATGGTAATATCCAAGCTTCCAAG                         GCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
genomic: AGCGTGAATCTGGAAGTAAGGTTCATCATGGTAATATCCAAGCTTCCAAGgtaaattaat ... tgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
EST: gi|124914607|gb|EH988481.1|EH988481
EST:     TATCCAAGCTTCCAAG                         GCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG
genomic: TATCCAAGCTTCCAAGgtaaattaat ... tgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcttgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG
                                      ttgttttt  CT-rich tract
                                      ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaatccttttctatggctctttttctctgtgatgcttgttgcttctctcctctggtttcagatcatcgttgtttttgtggtacagGCTGTTGCTGATATCATTCGTACAACATTGGGTCCTCGTTCTATGTTGAAGATGCTTCTTGATGCTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG