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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaagagttttcctcttttctttattcggttgctggttgcacataagtcggaaagatacttaccattcctcgtgcttcttttcctgtacgacattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCT

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_197V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 9
gtaagagttttcctcttttctttattcggttgctggttgcacataagtcggaaagatacttaccattcctcgtgcttcttttcctgtacgacattgt-tagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCT
|||  | ||||       | | |||||  ||   |  |  |    |    |||  |   ||    ||  | |   |     || |    |  ||| | |||||||| |  ||||| || |||||||| || |||      || || ||  | |||||||||||||| |||||||||||||| || || ||  | || ||||
gtattaattttgtctaaatatatattcatttaaggtctaaattctaccttgaataagttttggt-ttgtttgaagtctgactcttaattgtaattctgtagGTTGATCAAATGGTTATTCATTCTGCTTCAGATTTTCGGCCACGGACAACTCTCTGTGGTGATTACTTTTATAATTATTTTACTCGTGGTCTGGACATCT
















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|208382909|gb|DC928334.1|DC928334
EST:     GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG                         GTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCA
genomic: GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAGgttagttctt ... acattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCA
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG                         GTTGACCCTATGGTGATCCATTCTGCCTNTGATCCAAAACCTCGCACTGCA
genomic: GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAGgttagttctt ... acattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCA
EST: gi|6167306|gb|AW145570.1|AW145570
EST:     GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAG                         GTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCA
genomic: GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAGgttagttctt ... acattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCA
EST: gi|37821349|gb|BJ579415.1|BJ579415
EST:     CACCAGAAACCAG                         GTTGACCCTATGGTGATCCATTCTGCNTNTGATCCAAAACCTCGCACTGC
genomic: CACCAGAAA-CAGgttagttctt ... acattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGC

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: 34 (upstream exon), 23 (downstream exon)
Score: 6

GATGTGTGGGCAGAGTTAGGTCGGCCATGTGGTATTCACCAGAAACAGgttagttctt ... acattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcggaaagatacttaccattcctcgtgcttcttttcctgtacgacattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCT
           tacttac  putative branch site (score: 6)
      aaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagttttcctcttttctttattcggttgctggttgcacataagtcggaaagatacttaccattcctcgtgcttcttttcctgtacgacattgttagGTTGACCCTATGGTGATCCATTCTGCCTCTGATCCAAAACCTCGCACTGCACTCTGTGGTGATTATTTTTATAATTATTTCACACGCGGCATTGATATCT

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