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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctagcgtattcttttaaaactatctaattcagaaagagatgctgaaaggatatcagtgaccatttcttagggctgaatcgtgtctcttggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCTGATCTTCCACAAAATTCGAGCCGTATTTGGTTATGGGCTATGATTCGTT

Basic information

species Physcomitrella patens
transcript PP1S78_210V6.2
intron # 4
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|67695361|gb|BJ955594.1|BJ955594
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162208442|gb|FC384197.1|FC384197
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162199764|gb|FC375837.1|FC375837
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|18341071|gb|BJ173104.1|BJ173104
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162167356|gb|FC343059.1|FC343059
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAA
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAA
EST: gi|162167355|gb|FC343058.1|FC343058
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162249723|gb|FC428163.1|FC428163
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|208346478|gb|DC917431.1|DC917431
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|18333668|gb|BJ165683.1|BJ165683
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162179662|gb|FC355720.1|FC355720
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|37850040|gb|BJ608048.1|BJ608048
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162185883|gb|FC360983.1|FC360983
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
EST: gi|162185882|gb|FC360982.1|FC360982
EST:     GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG                         ATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT
genomic: GGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCT

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), 33 (downstream exon)
Score: 32

GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAGgtacacaatt ... ggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCTGATCTTCCACAAAATTCGAGCCGTATTTGGTTATGGGCTATGATTCGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaggatatcagtgaccatttcttagggctgaatcgtgtctcttggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCTGATCTTCCACAAAATTCGAGCCGTATTTGGTTATGGGCTATGATTCGTT
                                       tctcttg  CT-rich tract
                  atttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctagcgtattcttttaaaactatctaattcagaaagagatgctgaaaggatatcagtgaccatttcttagggctgaatcgtgtctcttggactcacagATACGGCAATGCAACAGTTGTGGAAAATACGGAGAGGGGCTGGAAAGATCTGATCTTCCACAAAATTCGAGCCGTATTTGGTTATGGGCTATGATTCGTT

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