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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaaagttattgtcttttgtcttgtgcttggtgttttctttatatggttgattaaaagtttgtgtttttttggtgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAGTCATGACAACACCAGATGGAAGAGTTTTGGATATGTTTTTCATCACTGA

Basic information

species Arabidopsis thaliana
transcript AT2G39570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g00740.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgtaaa-gttattgtcttttgtcttgtgcttggtgttttctttatatggttgattaaaagtttgtgtttttttggtgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAGTCATGACAACACCAGATGGAAGAGTTTTGGATATGTTTTTCATCACTGA
|||  |  ||| || |||   | || | ||  ||||  || ||| | || |       | | | | ||||    ||       || |||||||| || |||||  |  | ||||| |||||||||||  ||||||| ||||| |||||||| || ||||| ||||| |||||  | || |||||||| ||
gtaattacaaatgtcattccttattatttttggctttatgatttatgtaaaaatcacctgacatggttgttgcatt-------tttgtagATGTCACCAAAGTCCTCTCTGAGCTCGAGTTTACAATTGAAAGAGTAAAAGTGATGACAACCCCTGATGGCAGAGTCTTGGACCTTTTCTTCATCACGGA
















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|164048818|gb|ES069154.1|ES069154
EST:     CCGTGATAGGAAAGGATTGCTTCATG                         ATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG
genomic: CCGTGATAGGAAAGGATTGCTTCATGgtatgtgtaa ... tgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG
EST: gi|124913176|gb|EH987050.1|EH987050
EST:     CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATG                         ATGTTACTAAAGTTTTGA
genomic: CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATGgtatgtgtaa ... tgattcgtagATGTTACTAAAGTTTTGA
EST: gi|125299519|gb|EL313604.1|EL313604
EST:     CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATG                         ATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG
genomic: CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATGgtatgtgtaa ... tgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG
EST: gi|125075747|gb|EL139173.1|EL139173
EST:     GCCGTGATAGGAAAGGATTGCTTCATG                         ATGTTTACTAAAGTTTTGTACAGAGCTAGAGTTTACAATACAAAGAGTCAA
genomic: GCCGTGATAGGAAAGGATTGCTTCATGgtatgtgtaa ... tgattcgtagATG-TTACTAAAGTTTTG-ACAGAGCTAGAGTTTACAATACAAAGAGTCAA
EST: gi|301502493|gb|HO208033.1|HO208033
EST:     CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATG                         ATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG
genomic: CCTTTATCTTCTCAAGTTCTTTTGCCGTGATAGGAAAGGATTGCTTCATGgtatgtgtaa ... tgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgttttctttatatggttgattaaaagtttgtgtttttttggtgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAGTCATGACAACACCAGATGGAAGAGTTTTGGATATGTTTTTCATCACTGA
                 ggttgat  putative branch site (score: 5)
                      attaaaagtttgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaaagttattgtcttttgtcttgtgcttggtgttttctttatatggttgattaaaagtttgtgtttttttggtgattcgtagATGTTACTAAAGTTTTGACAGAGCTAGAGTTTACAATACAAAGAGTCAAAGTCATGACAACACCAGATGGAAGAGTTTTGGATATGTTTTTCATCACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA