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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcaagttacttgattcatcttttacttatatgcgttaacttctgtaattttggactaaaactcaatatggatgctttgatttggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATACAGACATGGTCTAACTCCTCCAATGAAGGATGCTCGAAAGAGGAGATTTC

Basic information

species Arabidopsis thaliana
transcript AT1G55300.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55300.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
gtaaaatcaagttacttgattcatcttttacttatatgcgttaacttctgtaattttggactaaaactcaatatggatgctttgatttggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATACAGACATGGTCTAACTCCTCCAATGAAGGATGCTCGAAAGAGGAGATTTC
||||||  |    | ||| || |  | |   ||||                |||| | | ||     | || |    | | |||| || | | ||||||||| ||||| || ||    | ||||||||| ||  |   | ||||||||| ||||||||| ||||||||||||| |||||| |||| | || | || |
gtaaaaggataagatttgtttaagatctgttttat---------------caattgtaggct----tttaagaatcttacattgagtttgta-acagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
















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|125242094|gb|EL256179.1|EL256179
EST:     GTGCATTAGTCAAAACTGCTGATATTGGGCAG                         ATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAG
genomic: GTGCATTAGTCAAAACTGCTGATATTGGGCAGgtaaaatcaa ... tggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAG
EST: gi|124944626|gb|EL020709.1|EL020709
EST:     TCAAAACTGCTGATATTGGGCAG                         ATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATAC
genomic: TCAAAACTGCTGATATTGGGCAGgtaaaatcaa ... tggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATAC
EST: gi|124763769|gb|EH853899.1|EH853899
EST:     TTAAAACTTATGATGATTGTGCATTAGTCAAAACTGCTGATATTAGGCAG                         ATGATCATGGTTAGGGAGCCT
genomic: TTAAAACTTATGATGATTGTGCATTAGTCAAAACTGCTGATATTGGGCAGgtaaaatcaa ... tggcacacagATGATCATGGTTAGGGAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttctgtaattttggactaaaactcaatatggatgctttgatttggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATACAGACATGGTCTAACTCCTCCAATGAAGGATGCTCGAAAGAGGAGATTTC
      tgtaatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcaagttacttgattcatcttttacttatatgcgttaacttctgtaattttggactaaaactcaatatggatgctttgatttggcacacagATGATCATGGTTAGGGAGCCTGGTGATCCTGCGCCTAATACAGTTGAATACAGACATGGTCTAACTCCTCCAATGAAGGATGCTCGAAAGAGGAGATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT