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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTGGTTGTAGGTGGAGGTTACATTGGGCTGGAATTAGCTGCATGTCTGACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactcttaccaaattgagtcaatatgttttttgacataagcttcaagtacctgttctgaacagaatagtgattctacaaactgaattgtgtggagaatgatcttcagaatcacaacaagtttcatatgcaagccctataaaagtatgagggggttgtttcttgttgacag

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
intron # 7
splice site 5'
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|100391837|gb|BY989572.1|BY989572
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162278698|gb|FC454808.1|FC454808
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|208385252|gb|DC915052.1|DC915052
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACNAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|208361425|gb|DC935112.1|DC935112
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162181159|gb|FC357604.1|FC357604
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|100363976|gb|BY966264.1|BY966264
EST:     ACGATGAAACA-GACTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTG
genomic: ACGATGAA-CAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTG
EST: gi|208375453|gb|DC936996.1|DC936996
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTNACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162225064|gb|FC401688.1|FC401688
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|208392192|gb|DC957271.1|DC957271
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|100378191|gb|BY949726.1|BY949726
EST:     CGATGAAACA-GATTNAAAGTCA-CATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTTACACC-GAACTTTGC-TCATTTTACGAGAGATACTA
genomic: CGATGAA-CAAGATT-AAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTT-ACACCCGAACTT-GCCTCATTTTACGAGAGATACTA
EST: gi|162178358|gb|FC355180.1|FC355180
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|100375395|gb|BY948855.1|BY948855
EST:     CGATGAAACA-GATTTAAAGTCA-CATGGTGTTCCCAGAAACATGCTTGA                         TGCCTCGTTTGTTNACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: CGATGAA-CAAGATT-AAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162237033|gb|FC413192.1|FC413192
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162221161|gb|FC397802.1|FC397802
EST:     GATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|100418007|gb|BY993291.1|BY993291
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
EST: gi|162158960|gb|FC334820.1|FC334820
EST:     GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGA                         TGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG
genomic: GACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATG

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), 34 (downstream exon)
Score: 34

GCAGTGGTTGTAGGTGGAGGTTACATTGGGCTGGAATTAGCTGCATGTCTGACGATGAACAAGATTAAAGTCAACATGGTGTTCCCAGAACCATGCTTGAgtaagactct ... ttgttgacagTGCCTCGTTTGTTTACACCCGAACTTGCCTCATTTTACGAGAGATACTATGAGGGTAAAGGCGTAAACATCATCAAGGGAACAACTGTAACTGCATTTGA




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