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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagcaccttttacctggtgcggtaatttgtgtcgagttctgaagcagtttcactaacgtggaatatggacttgaatgttttttctttgtaaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCATCATCTGAAGTTGCACAACCACGCAGATCAAATTCACAACGCTGTACTCA

Basic information

species Physcomitrella patens
transcript PP1S199_33V6.1
intron # 6
splice site 3'
intron type U2

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|162171537|gb|FC347839.1|FC347839
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|18340057|gb|BJ172085.1|BJ172085
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|67726238|gb|BJ976497.1|BJ976497
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162246372|gb|FC419934.1|FC419934
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162174845|gb|FC351637.1|FC351637
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|37853210|gb|BJ611218.1|BJ611218
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162235877|gb|FC411620.1|FC411620
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|67725138|gb|BJ975397.1|BJ975397
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|67696691|gb|BJ956924.1|BJ956924
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162261041|gb|FC437435.1|FC437435
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|208375010|gb|DC956406.1|DC956406
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162182686|gb|FC359433.1|FC359433
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|208361101|gb|DC957552.1|DC957552
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|37848893|gb|BJ606901.1|BJ606901
EST:     TCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|37836533|gb|BJ594541.1|BJ594541
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|18336310|gb|BJ168332.1|BJ168332
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCA
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGAC-GGCCCTGTTGTTGAGCTCTGTGATGATGCTGCA
EST: gi|162155666|gb|FC331279.1|FC331279
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162261042|gb|FC437436.1|FC437436
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|37826181|gb|BJ584193.1|BJ584193
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGNTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|67724281|gb|BJ974540.1|BJ974540
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|37844324|gb|BJ602332.1|BJ602332
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|162174844|gb|FC351636.1|FC351636
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|208385227|gb|DC923593.1|DC923593
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
EST: gi|208367531|gb|DC954963.1|DC954963
EST:     TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG                         AATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT
genomic: TGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCAT

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), 27 (downstream exon)
Score: 14

TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAGgttgttttct ... aaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCATCATCTGAAGTTGCACAACCACGCAGATCAAATTCACAACGCTGTACTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttcactaacgtggaatatggacttgaatgttttttctttgtaaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCATCATCTGAAGTTGCACAACCACGCAGATCAAATTCACAACGCTGTACTCA
      cactaac  putative branch site (score: 14)
                             aatgttttttctttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagcaccttttacctggtgcggtaatttgtgtcgagttctgaagcagtttcactaacgtggaatatggacttgaatgttttttctttgtaaaaaaacagAATATGGCCAATCCGACGGCCCTGTTGTTGAGCTCTGTGATGATGCTGCATCATCTGAAGTTGCACAACCACGCAGATCAAATTCACAACGCTGTACTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA