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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattataacagaacggttgtgatgtccatgccacagaacatttcctgaattgtctaatttcaaatagttcaccggtatgcttggtatggaaaatccagtctgtatttgttgatttgtttatggtttcatcgtcagcacaaggctgaatataacgagatttttcatttatcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.2
intron # 5
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|15261762|gb|BI437072.1|BI437072
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|100413810|gb|BY974995.1|BY974995
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTCTTGGCTGGAGAACTGACCCCGTTTCGCAGATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162254392|gb|FC430527.1|FC430527
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162230556|gb|FC407146.1|FC407146
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162263114|gb|FC439780.1|FC439780
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162256673|gb|FC433191.1|FC433191
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162249688|gb|FC426516.1|FC426516
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|208398676|gb|DC916199.1|DC916199
EST:     GCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAG-TTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: GCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|100431989|gb|BY978609.1|BY978609
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|7047275|gb|AW477169.1|AW477169
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162248897|gb|FC422891.1|FC422891
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162270571|gb|FC446496.1|FC446496
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162262523|gb|FC439735.1|FC439735
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162185364|gb|FC360938.1|FC360938
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|15262155|gb|BI437465.1|BI437465
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|100413123|gb|BY992598.1|BY992598
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162273997|gb|FC450344.1|FC450344
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|18363630|gb|BJ195702.1|BJ195702
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
EST: gi|162257577|gb|FC433711.1|FC433711
EST:     CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG                         CAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA
genomic: CCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCA

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: 41

CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAGgtaaaattat ... atcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcatcgtcagcacaaggctgaatataacgagatttttcatttatcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG
                        atataac  putative branch site (score: 41)
                                agatttttcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattataacagaacggttgtgatgtccatgccacagaacatttcctgaattgtctaatttcaaatagttcaccggtatgcttggtatggaaaatccagtctgtatttgttgatttgtttatggtttcatcgtcagcacaaggctgaatataacgagatttttcatttatcgttgcagCAATTTTCGGAGAAGTTTTTGGCTGGAGAACTGACCCCGTTTCGCAAATCACAGAGCCCTCCAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG