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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCGATGTCCTCGACTCCGCTCTTCTCCGACCTGGACGATTCGACAGGCAGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgccttgagttctttctacttcaatacaccatcctatctgcagcctcttttctcaacttgattatgcttctatcttatcgaatgctctcttgtcttaatccttacgaatttgcatttatggctttcttcatgagttcagcagaaattgtatactgatgaagaagttggtttccag

Basic information

species Physcomitrella patens
transcript PP1S44_78V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_78V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G126361_T01 (Zea mays), 5'ss of exon 1
ACCCGATGTCCTCGACTCCGCTCTTCTCCGACCTGGACGATTCGACAGGCAGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgccttgagttctttctacttcaatacaccatcctatctgcagcctcttttctcaacttgattatgcttctatcttatcgaatgctctcttgtcttaatccttacgaatttgcatttatggctttcttcatgagttcagcagaaattgtatactgatgaagaagttggtttccag
 |||||||| || |||||||| || || ||||| ||  |||| || |||||||| ||||||||||||||||| |||   || || ||||  |||||| ||||   ||   |||  || | | |||       || | ||| |         |||  ||     |   |||||||||    ||      |   |   |   | ||   ||                                                                       
GCCCGATGTGCTGGACTCCGCGCTCCTACGACCAGGGAGATTTGATAGGCAGGTCACCGTTGACAGGCCAGATGTTGCCGGACGCGTCAAGATTCTTGAGgtcagtga--tgaactcctgccact-------actagcctgtaaatttgtgcttagctagcagttgatatgcttctgaactactagtagtattgaggaacttatttata-----------------------------------------------------------------------
















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|162227325|gb|FC403917.1|FC403917
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162159396|gb|FC334664.1|FC334664
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162267864|gb|FC444465.1|FC444465
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|19789489|gb|BQ041335.1|BQ041335
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162180447|gb|FC355868.1|FC355868
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162215553|gb|FC391346.1|FC391346
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162166771|gb|FC342740.1|FC342740
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|100376379|gb|BY986138.1|BY986138
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162163190|gb|FC340244.1|FC340244
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162179553|gb|FC356593.1|FC356593
EST:     AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: AGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
EST: gi|162183816|gb|FC360733.1|FC360733
EST:     GTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAG                         GTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT
genomic: GTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATT

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: 34 (upstream exon), 35 (downstream exon)
Score: 30

ACCCGATGTCCTCGACTCCGCTCTTCTCCGACCTGGACGATTCGACAGGCAGGTTACCGTTGACAGGCCAGACGTTCAAGGTCGTGTCAGAATTCTTCAGgtacatgcct ... tggtttccagGTTCACTCTCGTGGAAAGACATTGGCCAAGGATGTCGATTTCGAGAAGATTGCAAGGAGGACACCAGGGTTCACCGGTGCCGACCTACAGAACTTGATGA




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