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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggcttttgcccttgctctcgctgcttgcattgtttgagattggcatttgccgcagtcaatgacgtgctgcatagggttagctttctggggcgca...

Basic information

species Physcomitrella patens
transcript PP1S101_170V6.2
intron # 2
splice site 5'
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|100362130|gb|BY966347.1|BY966347
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|18374490|gb|BJ206068.1|BJ206068
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|18350839|gb|BJ182890.1|BJ182890
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100447629|gb|CJ971928.1|CJ971928
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208376645|gb|DC932109.1|DC932109
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|18360844|gb|BJ192907.1|BJ192907
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100357299|gb|BY983792.1|BY983792
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|18365279|gb|BJ197353.1|BJ197353
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|67712836|gb|BJ966285.1|BJ966285
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGNCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|18350558|gb|BJ182609.1|BJ182609
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100446549|gb|CJ970848.1|CJ970848
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208360268|gb|DC943012.1|DC943012
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|67718552|gb|BJ968811.1|BJ968811
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100365424|gb|BY966589.1|BY966589
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100400204|gb|BY990831.1|BY990831
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|100425961|gb|BY977207.1|BY977207
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208371115|gb|DC931575.1|DC931575
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|67719511|gb|BJ969770.1|BJ969770
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208359545|gb|DC934574.1|DC934574
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|67718199|gb|BJ968458.1|BJ968458
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208377442|gb|DC902771.1|DC902771
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|162154878|gb|FC331920.1|FC331920
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
EST: gi|208390264|gb|DC942015.1|DC942015
EST:     AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGG                         ACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT
genomic: AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGAT

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: 33 (upstream exon), 31 (downstream exon)
Score: 19

AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggct ... ttggtggtagACATGAGCTTTTGATGTTCGAGGCTCTGCGGGAGGGGCTTGGCGAGGAGATGGAGCGGGACCCGAACGTGTGCGTTATTGGGGAGGATGTGGGAGACTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAAGGAGGCTGTGTCATCGTCGTCGTCGAGCCAGGGAGGgtgagtggcttttgcccttgctctcgctgcttgcattgtttgagattggcatttgccgcagtcaatgacgtgctgcatagggttagctttctggggcgca

-  AAGGAG