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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagagcttaccttgttccttgaaaatgaactgtgcctagagaattccttcatgtcttttatgaggtctttttctcaagcataaagacccttagatctacgttccttgtttatgcgtactattcgtaatcgaatctggtggtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATG

Basic information

species Physcomitrella patens
transcript PP1S90_13V6.1
intron # 10
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|208396230|gb|DC924024.1|DC924024
EST:     ATCGATGCCC-TTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: ATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|162199310|gb|FC375146.1|FC375146
EST:     CAGGGATTTTCTGCGAGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: CAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|22132775|gb|BQ827349.1|BQ827349
EST:     CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTACTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|162190182|gb|FC365924.1|FC365924
EST:     CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|162190181|gb|FC365923.1|FC365923
EST:     AGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: AGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|162162473|gb|FC339204.1|FC339204
EST:     CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|208367676|gb|DC947368.1|DC947368
EST:     ATCGATG-CCNTTNTCACCAGGGATTTT-TGCGAGTGTTGCTCAG                         TGGATGACGACCAAC-TGAAAGCTGCCNAAGCAGAAGGTCGTTCAGGATAT
genomic: ATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|162186442|gb|FC362998.1|FC362998
EST:     CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
genomic: CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT
EST: gi|22132757|gb|BQ827332.1|BQ827332
EST:     CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTACTCAG                         TGGATGACGACAAACTTGAAAGCTGCCAAAGTAGAAGGTCGTTCAGGATAT
genomic: CTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATAT

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), 33 (downstream exon)
Score: 31

CTTCCTTCAAGAAGATCTTTAATCGATGCCCTTTCTCACCAGGGATTTTCTGCGAGTGTTGCTCAGgttgagagct ... gtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacgttccttgtttatgcgtactattcgtaatcgaatctggtggtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATG
                                              tttgctt  CT-rich tract
          ttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgagagcttaccttgttccttgaaaatgaactgtgcctagagaattccttcatgtcttttatgaggtctttttctcaagcataaagacccttagatctacgttccttgtttatgcgtactattcgtaatcgaatctggtggtttgcttagTGGATGACGACAAACTTGAAAGCTGCCAAAGCAGAAGGTCGTTCAGGATATGAGTGGGTGTTTGATCTGGAAGGCATCGCTGACATGTATAAATCCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG