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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactaatctgttcctcttggaaattccgcttagttggttaattactatcagagaataccgtccatgaacaaactgatactcatgttcattctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAATGTGCAACGGCGTCTGGATCATGAAGGAGCGTGAAATTTTGACGGTTGAT

Basic information

species Physcomitrella patens
transcript PP1S61_277V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_277V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G439578_T01 (Zea mays), 3'ss of exon 6
gtaagtactaatctgt-tcctcttggaaattccgcttagttggttaattactatcagagaataccgtccatgaacaaactgatactcatgttcattctcgatgc--agAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAATGTGCAACGGCGTCTGGATCATGAAGGAGCGTGAAATTTTGACGGTTGAT
       || || | | ||   || |  ||   ||   | |  |       | |   |       ||     |  | ||| |       |    | |   ||||  || ||||| ||||||||| |||||||||| ||||||||  ||||||| || |||||||| ||    |||||||||||||| | | ||||  |||   |  ||
-------ctgatatatatctagttagttatctagccgtgcttttgggcctttgtttcattg-gttgtttggcataacacttacctctccggctctccctaatgcacagCATTGCCAACATTGTCTACTGCATGCGGACAGAGAATATTGAGTCTGTTATGTGCAATGGTCGGTGGATCATGAAGGATCATAAAATCATGAATCTCAAT
















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|67698086|gb|BJ958319.1|BJ958319
EST:     TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCC                         AATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
genomic: TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCCgtaagtacta ... ctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
EST: gi|208365600|gb|DC944098.1|DC944098
EST:     TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCC                         AATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
genomic: TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCCgtaagtacta ... ctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
EST: gi|162176344|gb|FC353529.1|FC353529
EST:     TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCC                         AATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
genomic: TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCCgtaagtacta ... ctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
EST: gi|67574672|gb|BJ947496.1|BJ947496
EST:     TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCC                         AATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT
genomic: TTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCCgtaagtacta ... ctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAAT

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: 35 (upstream exon), 31 (downstream exon)
Score: 8

GCAGACTTCGTGATCCTCAACCTTGACCTATGGACGATGGTGCCTCTTCTTGACCCgtaagtacta ... ctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAATGTGCAACGGCGTCTGGATCATGAAGGAGCGTGAAATTTTGACGGTTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcagagaataccgtccatgaacaaactgatactcatgttcattctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAATGTGCAACGGCGTCTGGATCATGAAGGAGCGTGAAATTTTGACGGTTGAT
                         aactgat  putative branch site (score: 8)
                                       ttcattctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactaatctgttcctcttggaaattccgcttagttggttaattactatcagagaataccgtccatgaacaaactgatactcatgttcattctcgatgcagAATTGCAAACATTGTCAACTGCATGCGCACAGAGAACGTTGAGTCAGTAATGTGCAACGGCGTCTGGATCATGAAGGAGCGTGAAATTTTGACGGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG