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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccatgatccttacttgtctctccacactcctcttgtacgtcattgtatctgtaacaaatttgagtttctatgacgttttttaagcatatgtgtgtgtttttgtgatatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAATTGTCTTCATTGCAAG

Basic information

species Physcomitrella patens
transcript PP1S6_375V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_375V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 16
gtatgccatgatccttacttgtctctccacactcctcttgtacgtcattgtatctgtaacaaatttgagtttctatgacgttttttaagcatatgtgtgtgtttttgtgatatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAATTGTCTTCATTGCAAG
    |  | ||     | ||| |  | |  |||    |   |  | |   ||    |||  | |    |     |  | | ||  ||| ||  | ||      |   || | | || ||||||||| || |||||||| | | |   |||  |  | || |||||||||||||||||||||||||||
----gtaagga-----aattggcctttcttacttgaatgaaagataacc-tacaattaagtactgaatgcccaaacaaggattgctaatcacttctgc---catacatgttctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG
















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|7287107|gb|AW599594.1|AW599594
EST:     CCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
EST: gi|37822904|gb|BJ580970.1|BJ580970
EST:     CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
EST: gi|162272490|gb|FC448492.1|FC448492
EST:     CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
EST: gi|37840081|gb|BJ598089.1|BJ598089
EST:     CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
EST: gi|162179801|gb|FC356392.1|FC356392
EST:     CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
EST: gi|7207408|gb|AW561410.1|AW561410
EST:     CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGA                         GTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA
genomic: CCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAA

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: 32 (upstream exon), 20 (downstream exon)
Score: 5

CACCACATTTGCGTCTACGTGACCCTCAAATTCCTGAATCTGTAAATTTACCTAAATACGCAGGGCCAGAGTCCCGATACTGCCCAGCTCGAGTATACGAgtatgccatg ... tatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAATTGTCTTCATTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtttctatgacgttttttaagcatatgtgtgtgtttttgtgatatgattcagGTATGTTACGGACGAGAATGATAAAATGAAATTGAATATTAATGCTCAAAATTGTCTTCATTGCAAG
               ttttttaagcatat  TA-rich tract