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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACGGGGATAAGAAGGTTTTCGGAGGCAAGGGTGTGTTGAAGGCTGTGGATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggttgcgggcagtttgggaggatgaattggtatacagagtgatcttgcattgaacttggtagcagctcgtgctggttggtacaggtgtgtgatgagattattgctgggagggtttggataactgtatattggtggaaatcgcag

Basic information

species Physcomitrella patens
transcript PP1S76_97V6.1
intron # 1
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|67574786|gb|BJ947610.1|BJ947610
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208358241|gb|DC930682.1|DC930682
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCANAAAGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100422653|gb|BY976481.1|BY976481
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208391200|gb|DC942084.1|DC942084
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208386660|gb|DC929106.1|DC929106
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100451488|gb|CJ974791.1|CJ974791
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|162219390|gb|FC396413.1|FC396413
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208355566|gb|DC929886.1|DC929886
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208394416|gb|DC942576.1|DC942576
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100407260|gb|BY974083.1|BY974083
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTANTGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100386992|gb|BY951391.1|BY951391
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208363829|gb|DC943286.1|DC943286
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|162174157|gb|FC350360.1|FC350360
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208391064|gb|DC929376.1|DC929376
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100385604|gb|BY987669.1|BY987669
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208369545|gb|DC936321.1|DC936321
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208392668|gb|DC938591.1|DC938591
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|162166358|gb|FC342340.1|FC342340
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|162214126|gb|FC389964.1|FC389964
EST:     GGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|67709517|gb|BJ965333.1|BJ965333
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100361685|gb|BY947771.1|BY947771
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|162185552|gb|FC361484.1|FC361484
EST:     GGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|18374746|gb|BJ206324.1|BJ206324
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|208384471|gb|DC911557.1|DC911557
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|67573809|gb|BJ946633.1|BJ946633
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
EST: gi|100390992|gb|BY953002.1|BY953002
EST:     GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCG                         GAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA
genomic: GATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAA

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: 26 (upstream exon), 35 (downstream exon)
Score: 9

GGGACGGGGATAAGAAGGTTTTCGGAGGCAAGGGTGTGTTGAAGGCTGTGGATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggt ... gaaatcgcagGAATCAGAAGGAGATTGACAGCGTAATGCTAGAATTGGATGGCTCGCCCAACAAGGGTAACCTGGGCGCCAATGCCATCTTGGGTTTGTCTTTGAGCGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACGGGGATAAGAAGGTTTTCGGAGGCAAGGGTGTGTTGAAGGCTGTGGATAATATTAACAATGTATTGGCGAAGAAGCTTGTGGGGCTTGATACTCGgtgagttggttgcgggcagtttgggaggatgaattggtatacagagtgatcttgcattgaacttggtagcagctcgtgctggttggtacaggtgtgtgatgagattattgctgggagggtttggataactgtatattggtggaaatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC