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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattgacttctcaaaacttgataacattcttgaagtgctgagcatgtattggtgattgcaaattagttctaggacgggagaggcctttaaatcaga...

Basic information

species Physcomitrella patens
transcript PP1S83_44V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_44V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
ACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattgacttctcaaaacttgataacattcttgaagtgctgagcatgtattggtgattgcaaattagttctaggacgggagaggcctttaaatcaga
|||| ||| | |||||||| ||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||  |||| || ||||| ||||| ||||||||  |||   ||||         | |  ||| |  | ||  |||  |||      | ||   |   |  |  || |            |||    ||| 
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtcta-gta-tgaaaatgaggcaatcatcttatgctcttattatg-----------ttttgttccag-
















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|162182876|gb|FC359779.1|FC359779
EST:     ATCAGCGATTTGTGTGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|208389513|gb|DC945779.1|DC945779
EST:     ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|162167331|gb|FC342319.1|FC342319
EST:     ATCAGCGATTTGTGTGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|18335291|gb|BJ167309.1|BJ167309
EST:     GTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: GTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|208371954|gb|DC951931.1|DC951931
EST:     ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|162182877|gb|FC359780.1|FC359780
EST:     ATCAGCGATTTGTGTGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|162160957|gb|FC336994.1|FC336994
EST:     ATCAGCGATTTGTGTGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
EST: gi|67723757|gb|BJ974016.1|BJ974016
EST:     ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAG                         TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC
genomic: ATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 19 (upstream exon), 29 (downstream exon)
Score: 5

ACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattga ... tggataacagTGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAACGGCTCCTGATATTGCTGGCAAG




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