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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttctttgttgccgatttctatgtacaatgggttgaatgtgggtagaggaatgcttggggtgtgttgacgacatcgctctgttttggttcgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 1
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|162179835|gb|FC355906.1|FC355906
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|162182305|gb|FC357176.1|FC357176
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18369273|gb|BJ201358.1|BJ201358
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|100385980|gb|BY951174.1|BY951174
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18365567|gb|BJ197644.1|BJ197644
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18362808|gb|BJ194880.1|BJ194880
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|208358811|gb|DC935197.1|DC935197
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|100428360|gb|BY977766.1|BY977766
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18361307|gb|BJ193373.1|BJ193373
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18374142|gb|BJ205720.1|BJ205720
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18360348|gb|BJ192410.1|BJ192410
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18369196|gb|BJ201281.1|BJ201281
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTANTAAT                         ACTGCGGTTGCTTCAGANTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|208379665|gb|DC903720.1|DC903720
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCNAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|162155361|gb|FC331767.1|FC331767
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18356126|gb|BJ188185.1|BJ188185
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAANTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18366816|gb|BJ198896.1|BJ198896
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|100392460|gb|BY953374.1|BY953374
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
EST: gi|18370401|gb|BJ202003.1|BJ202003
EST:     TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAAT                         ACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
genomic: TGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG

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), 35 (downstream exon)
Score: 8

AGCGATGCGTCGCCTCGCTAGATCGCAGAGCCAGCACCTGCACCGCGCATTGCATCGAACCCCTCCTGCCGCCTGCTCCGGTTTCCGGTTCTCTAGTAATgttagtttct ... cgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaggaatgcttggggtgtgttgacgacatcgctctgttttggttcgtatcgcagACTGCGGTTGCTTCAGAGTACTCAAGTTCGGCTAAGTCGAATGTAACG
                  tgttgac  putative branch site (score: 8)