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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgtcagcggtgtgttacatggtccatgacatcgcagcaattccccttcatttagtttgaatctcctgactgagtttgttctacgttgattgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCATTGAATGGACTCTCAATTCTTGCTTTACAAGGCTTAATCTCGTGATCAT

Basic information

species Physcomitrella patens
transcript PP1S93_121V6.1
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|162166849|gb|FC343026.1|FC343026
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|18346547|gb|BJ178592.1|BJ178592
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|100435503|gb|BY960945.1|BY960945
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|18347192|gb|BJ179238.1|BJ179238
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|18373101|gb|BJ204703.1|BJ204703
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|100428589|gb|BY977883.1|BY977883
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGAC-GTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
EST: gi|18354707|gb|BJ186765.1|BJ186765
EST:     CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAG                         GGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA
genomic: CATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCA

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: 22 (upstream exon), 19 (downstream exon)
Score: 2

GGAGCTTGAAAACCGGCGGGCTTGTGAGACTGTTGCTGCTGCTGCAGTGCCATTGGTGTTGAGCGTGTATTCGTCGTTACGTTTGTCACCATCGATTTAGgtgagggaat ... attgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCATTGAATGGACTCTCAATTCTTGCTTTACAAGGCTTAATCTCGTGATCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttcatttagtttgaatctcctgactgagtttgttctacgttgattgcttcagGGCCTTGACTGTTGACGAAGCTACTGTATCAGCGGTGGAACAGACGAATCATTGAATGGACTCTCAATTCTTGCTTTACAAGGCTTAATCTCGTGATCAT
                                              ttgcttc  CT-rich tract
      atttagttt  TA-rich tract