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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcatttggctcttagcacaaactaagtcaattgattcgctgacttacggtatatcatttgttttgtgtgttttgttatttttttcttattttgtgcagATGCTGGACTATACTGTGCCTGGAG

Basic information

species Physcomitrella patens
transcript PP1S101_225V6.1
intron # 2
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|162152920|gb|FC329222.1|FC329222
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100387744|gb|BY951744.1|BY951744
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100427422|gb|BY977489.1|BY977489
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|67508001|gb|BJ940875.1|BJ940875
EST:     ATTCCGAGCTTGTCACATACNCGGAGGAGTCTCGTGCTTGGATTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100401204|gb|BY990883.1|BY990883
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100361028|gb|BY946877.1|BY946877
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|18368096|gb|BJ200181.1|BJ200181
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|162230234|gb|FC406590.1|FC406590
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100402689|gb|BY954960.1|BY954960
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100436231|gb|BY979445.1|BY979445
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100353340|gb|BY964757.1|BY964757
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|18358942|gb|BJ191001.1|BJ191001
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100443767|gb|BY963864.1|BY963864
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100427775|gb|BY977667.1|BY977667
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|208345511|gb|DC909201.1|DC909201
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG
EST: gi|100396655|gb|BY990233.1|BY990233
EST:     ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAG                         ATGCTGGACTATACTGTGCCTGGAG
genomic: ATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG

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), 25 (downstream exon)
Score: 22

GGAAAAGTTTATGGACGTTTACCAGCAGCTGAAGAAGGAGATTCTGTCTGATTCCGAGCTTGTCACATACACGGAGGAGTCTCGTGCTTGGGTTGAAGAGgtcacttggc ... ttttgtgcagATGCTGGACTATACTGTGCCTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacggtatatcatttgttttgtgtgttttgttatttttttcttattttgtgcagATGCTGGACTATACTGTGCCTGGAG
                          ttttgttatttttttc  CT-rich tract
                      tgtgttttgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcatttggctcttagcacaaactaagtcaattgattcgctgacttacggtatatcatttgttttgtgtgttttgttatttttttcttattttgtgcagATGCTGGACTATACTGTGCCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA