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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaggttatcccgtttctaattatgtcgaacttccttgtgcttgagttccatatgtgcaacaactgcggtatattgtagaggtcttatgacctatcaaactctttgtgacttattttatcttgcgtcattaatgccgacgagattccctttaaacgtgatggggattcttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTAACGAAGGATTTCCATATCTACCTCACACGCAATGGCCGCATCAG

Basic information

species Physcomitrella patens
transcript PP1S223_31V6.1
intron # 8
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|37847595|gb|BJ605603.1|BJ605603
EST:     TCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCNTGAGCAAGTAGATCGTTTA
genomic: TCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37840459|gb|BJ598467.1|BJ598467
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|7286670|gb|AW599157.1|AW599157
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCG
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCG
EST: gi|162214195|gb|FC390241.1|FC390241
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162192505|gb|FC371696.1|FC371696
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37845929|gb|BJ603937.1|BJ603937
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|208369208|gb|DC955837.1|DC955837
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37822610|gb|BJ580676.1|BJ580676
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37827861|gb|BJ585873.1|BJ585873
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162164021|gb|FC339309.1|FC339309
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162221031|gb|FC398283.1|FC398283
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162221032|gb|FC398284.1|FC398284
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162198688|gb|FC373469.1|FC373469
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162257989|gb|FC434083.1|FC434083
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|7286761|gb|AW599248.1|AW599248
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|208348127|gb|DC916937.1|DC916937
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|67724754|gb|BJ975013.1|BJ975013
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37852295|gb|BJ610303.1|BJ610303
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|37822517|gb|BJ580583.1|BJ580583
EST:     TCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: TCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|67725499|gb|BJ975758.1|BJ975758
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162256779|gb|FC432673.1|FC432673
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
EST: gi|162244629|gb|FC423452.1|FC423452
EST:     ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAG                         ATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA
genomic: ATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTA

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: 12 (upstream exon), 24 (downstream exon)
Score: 1

GGAATGGCTGACCGTATCATCGGCATGCGTGAGACACTCCGTACCAATCTTGAGAAGGCTGGATCTCAGCACAGCTGGAAGCATATCACTGATCAGgcaaggttat ... ttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTAACGAAGGATTTCCATATCTACCTCACACGCAATGGCCGCATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcattaatgccgacgagattccctttaaacgtgatggggattcttcggcgcagATTGGTATGTTTTGCTTCAGCGGTTTGAAGCCTGAGCAAGTAGATCGTTTAACGAAGGATTTCCATATCTACCTCACACGCAATGGCCGCATCAG
   cattaat  putative branch site (score: 1)
                                          ttcttc  putative PPT
                         tttaaa  TA-rich tract