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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagttcatctaggatttgcgattgcgcacttcgttgctaggtatttgcaccgatctcttgatgtagttatctaacctgttcaattttacgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTGAAGAAGGACAACGTCGCTCTTTACGTTAAG

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.2
intron # 1
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|208372110|gb|DC940292.1|DC940292
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|67703408|gb|BJ963641.1|BJ963641
EST:     CGTCCTCGGCTGCACTGACAGCCCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|67574849|gb|BJ947673.1|BJ947673
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18358247|gb|BJ190306.1|BJ190306
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCT
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCT
EST: gi|18374954|gb|BJ206532.1|BJ206532
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|67703063|gb|BJ963296.1|BJ963296
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCANAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|67570023|gb|BJ942847.1|BJ942847
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|100369975|gb|BY967466.1|BY967466
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18366753|gb|BJ198832.1|BJ198832
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|100397833|gb|BY990424.1|BY990424
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|208359935|gb|DC938956.1|DC938956
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|162167595|gb|FC343740.1|FC343740
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18358325|gb|BJ190384.1|BJ190384
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18372637|gb|BJ204239.1|BJ204239
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|100373109|gb|BY949215.1|BY949215
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|162157447|gb|FC333211.1|FC333211
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|100383769|gb|BY969298.1|BY969298
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18327150|gb|BJ159151.1|BJ159151
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|208364270|gb|DC935541.1|DC935541
EST:     CGTCCTCGGCTGCACTGACGGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18362471|gb|BJ194541.1|BJ194541
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|100358066|gb|BY965455.1|BY965455
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
EST: gi|18329338|gb|BJ161344.1|BJ161344
EST:     CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGG                         AGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG
genomic: CGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTG

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: 32 (upstream exon), 33 (downstream exon)
Score: 16

TGTTTCTTCCTTGACTCGTCGCTGTTAGATTGCAATGACTACAGCGATGGCGTCCTCGGCTGCACTGACAGCTCTTGCGAGCGGCCAAGAAGTTCTTCGGgtctgttacc ... cgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTGAAGAAGGACAACGTCGCTCTTTACGTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcaccgatctcttgatgtagttatctaacctgttcaattttacgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTGAAGAAGGACAACGTCGCTCTTTACGTTAAG
                         atctaac  putative branch site (score: 16)
                                   ttcaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagttcatctaggatttgcgattgcgcacttcgttgctaggtatttgcaccgatctcttgatgtagttatctaacctgttcaattttacgatgaatagAGTGGCGTTACGCAGAAGTTCTCTGGCCTTAGGGTTGCCGCTTTCCCTCTGAAGAAGGACAACGTCGCTCTTTACGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG