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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttaacgtttctgaaagctgcataatgtgctctttattctaagaatcaactgtttgtttggaacgggaagatttcgccgccatcgtatctttgcactaaatattgggcaaaactaatggttgctcaattcgcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTCTTGGATGAATCCAAGGATGTCGTTCTTGAG

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.2
intron # 6
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|162198842|gb|FC372869.1|FC372869
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|15261762|gb|BI437072.1|BI437072
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGATCATTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|18340941|gb|BJ172972.1|BJ172972
EST:     CAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: CAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|100413810|gb|BY974995.1|BY974995
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAGATCACAGAGCCCTCCTAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGACGAT-GT
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGA-GATTGT
EST: gi|162254392|gb|FC430527.1|FC430527
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162230556|gb|FC407146.1|FC407146
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162263114|gb|FC439780.1|FC439780
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162256673|gb|FC433191.1|FC433191
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162249688|gb|FC426516.1|FC426516
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162273996|gb|FC450343.1|FC450343
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|208398676|gb|DC916199.1|DC916199
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|100431989|gb|BY978609.1|BY978609
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|7047275|gb|AW477169.1|AW477169
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162248897|gb|FC422891.1|FC422891
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162270571|gb|FC446496.1|FC446496
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162262523|gb|FC439735.1|FC439735
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162185364|gb|FC360938.1|FC360938
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|37828074|gb|BJ586086.1|BJ586086
EST:     GCAAATCACAGAGCCNTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: GCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|15262155|gb|BI437465.1|BI437465
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|100413123|gb|BY992598.1|BY992598
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|208350976|gb|DC925981.1|DC925981
EST:     CTGGAGAACTGACCCCNTTTCGCAAATCACAGAGNCNTCCNAANGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACNTTCGACGAGATTGTC
genomic: CTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162273997|gb|FC450344.1|FC450344
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|18363630|gb|BJ195702.1|BJ195702
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
EST: gi|162257577|gb|FC433711.1|FC433711
EST:     TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG                         AACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC
genomic: TGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTC

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: 35 (upstream exon), 35 (downstream exon)
Score: 69

CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAGgtacgtttaa ... gcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTCTTGGATGAATCCAAGGATGTCGTTCTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctttgcactaaatattgggcaaaactaatggttgctcaattcgcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTCTTGGATGAATCCAAGGATGTCGTTCTTGAG
                         aactaat  putative branch site (score: 69)
                                              cgttctc  putative PPT
         actaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttaacgtttctgaaagctgcataatgtgctctttattctaagaatcaactgtttgtttggaacgggaagatttcgccgccatcgtatctttgcactaaatattgggcaaaactaatggttgctcaattcgcgttctcagAACGATGGACCAGTGAAGATTGTTGTATCTTCAACCTTCGACGAGATTGTCTTGGATGAATCCAAGGATGTCGTTCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG