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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacctgatgaatccttttgtgtaagatcagctgatatttaaaccattttccttctgaatcaatggttaatacttgtctctctttttgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTTGTTGCTGATGGCGGAGAATGCCTCGTTGCTCAAAGTTATGCGAAGAACA

Basic information

species Arabidopsis thaliana
transcript AT5G11520.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11520.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 5
gtacacctgatgaatccttttgtgtaaga-tcagctgatatt---taaaccattttccttctgaatcaatggttaatacttgtctctctttttgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTTGTTGCTGATGGCGGAGAATGCCTCGTTGCTCAAAGTTATGCGAAGAACA
|||  |  ||||     |   | | || | | |  ||| |||    ||| ||  |         ||  |    | || |   | | | | ||    |  |||||||||||||||||||||||||| | ||||||  |  |  |  | ||||||||||||||||| || |||   ||| | ||||| || || || |||||||
gtatgca-gatg-----tgcagagcaaaagtgacttgacattgcaaaaaacacatctggatcctatacactcatcattcacatttttttgttaacctgacagGGCTTTGCAAGTGGAAGTCTTGACAAAGATGCTCAGTCAGTGCGTATGTTTGTTGCTGATGGTGGTGAACTTCTCATGGCTCAGAGCTACGCTAAGAACA
















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|124821677|gb|EH906543.1|EH906543
EST:     AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAG                         GGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAA
genomic: AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAGgtacacctga ... tgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAA
EST: gi|301502657|gb|HO208197.1|HO208197
EST:     AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAG                         GGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT
genomic: AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAGgtacacctga ... tgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT
EST: gi|125190783|gb|EL205737.1|EL205737
EST:     CGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAG                         GGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT
genomic: CGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAGgtacacctga ... tgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT
EST: gi|301502679|gb|HO208219.1|HO208219
EST:     AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAG                         GGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT
genomic: AGTTGATGCGATCAAAGGGATTGATGCCCTTCTTCGATAGTGCTTATCAGgtacacctga ... tgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccattttccttctgaatcaatggttaatacttgtctctctttttgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTTGTTGCTGATGGCGGAGAATGCCTCGTTGCTCAAAGTTATGCGAAGAACA
                       ggttaat  putative branch site (score: 4)
                             tacttgtctctctttt  CT-rich tract
                         ttaatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacctgatgaatccttttgtgtaagatcagctgatatttaaaccattttccttctgaatcaatggttaatacttgtctctctttttgtatcgcagGGCTTTGCAAGTGGAAGTCTTGATACAGATGCGAAACCTATTAGGATGTTTGTTGCTGATGGCGGAGAATGCCTCGTTGCTCAAAGTTATGCGAAGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC