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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatggagtttttcggtaatggaggaatgattcctgggtttggaaatcgtcttgagggccttggaaattcaccttcactaattggcgttgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGCAATCTTGCTTCATCATCAGTCGACATCACTCTACTCGACTGCAGGCCCA

Basic information

species Physcomitrella patens
transcript PP1S61_112V6.1
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|18325546|gb|BJ157543.1|BJ157543
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18325546|gb|BJ157543.1|BJ157543
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18325546|gb|BJ157543.1|BJ157543
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|208376453|gb|DC902750.1|DC902750
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|208376453|gb|DC902750.1|DC902750
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|208376453|gb|DC902750.1|DC902750
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|162153960|gb|FC329467.1|FC329467
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|100376203|gb|BY986072.1|BY986072
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|18332323|gb|BJ164336.1|BJ164336
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|208371195|gb|DC931613.1|DC931613
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|18373593|gb|BJ205171.1|BJ205171
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|208385210|gb|DC911414.1|DC911414
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGCAG                       
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGG-C--CAGgttcctgagc ... tgtacagc
EST: gi|18359419|gb|BJ191480.1|BJ191480
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18359419|gb|BJ191480.1|BJ191480
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18359419|gb|BJ191480.1|BJ191480
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|162245923|gb|FC420811.1|FC420811
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|18330164|gb|BJ162170.1|BJ162170
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18330164|gb|BJ162170.1|BJ162170
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18330164|gb|BJ162170.1|BJ162170
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|100449571|gb|CJ973826.1|CJ973826
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|18367488|gb|BJ199571.1|BJ199571
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18367488|gb|BJ199571.1|BJ199571
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18367488|gb|BJ199571.1|BJ199571
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|100436177|gb|BY979418.1|BY979418
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|100436177|gb|BY979418.1|BY979418
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|100436177|gb|BY979418.1|BY979418
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|100415960|gb|BY957009.1|BY957009
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGCAG                       
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGG-C--CAGgttcctgagc ... tgtacagc
EST: gi|100449948|gb|CJ974017.1|CJ974017
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGCAG                       
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGG-C--CAGgttcctgagc ... tgtacagc
EST: gi|162191379|gb|FC368162.1|FC368162
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         GAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGC
EST: gi|67571782|gb|BJ944606.1|BJ944606
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGCAG                       
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGG-C--CAGgttcctgagc ... tgtacagc
EST: gi|18367178|gb|BJ199259.1|BJ199259
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18367178|gb|BJ199259.1|BJ199259
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-
EST: gi|18367178|gb|BJ199259.1|BJ199259
EST:     TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAG                         C
genomic: TTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcag-

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), 35 (downstream exon)
Score: 12

CCATACTCGATTGCTCATTGAAGACTTCATAGCCCATTTTGATGATTGTCTTGGATGATTCGTGAAGCTGGTGGAAGGGCTTCGTGACATACAGGGCCAGgttcctgagc ... tgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGCAATCTTGCTTCATCATCAGTCGACATCACTCTACTCGACTGCAGGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcgtcttgagggccttggaaattcaccttcactaattggcgttgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGCAATCTTGCTTCATCATCAGTCGACATCACTCTACTCGACTGCAGGCCCA
                                cactaat  putative branch site (score: 12)
                     aaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatggagtttttcggtaatggaggaatgattcctgggtttggaaatcgtcttgagggccttggaaattcaccttcactaattggcgttgtacagcagGAGTAGGACGAAAGAGTTTCGATTTCAATGTCCGCCGCCAGCTTGTTCTGCAATCTTGCTTCATCATCAGTCGACATCACTCTACTCGACTGCAGGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG