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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGTTGGACCCGAACCAGTACATCAACGCGATGCAACAAGTGATGCAAAATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagcgttcgttgggtggggtggttggtggagcagggaagggggtaggaagtgtatacggatgtgtgcggttagagtggtggcgtaggtgaaagg...

Basic information

species Physcomitrella patens
transcript PP1S8_3V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_3V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 5'ss of exon 4
CCAGTTGGACCCGAACCAGTACATCAACGCGATGCAACAAGTGATGCAAAATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcg-gtagcgttcgttg--ggtggggtggttggtggagcagggaagggggtagga-agtgtatacggatgtgtgcggttagagt--ggtggcgtaggtgaaagg
 ||||| ||| |  | |||||      | | ||||||||||| |||||||||||||| || ||||| ||||| || || || || || ||  | ||||||||  |  | |  ||   ||  | |   |   ||  ||    |         ||| || |   ||     || | |  | ||| | |   ||||| ||  |     |
ACAGTTTGACACACAACAGTATTATTCCACCATGCAACAAGTTATGCAAAATCCTCAATTTATGACTATGGCTGAGCGTCTTGGTAATGCATTAATGCAGgtttgtatggtctttcatgttgtttaagctatttctgtgttattattttatgtatgataaaataatatcatttttcagattaaatttcagtggcatattttttcag
















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|162203208|gb|FC379305.1|FC379305
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100399907|gb|BY990681.1|BY990681
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208383022|gb|DC927772.1|DC927772
EST:     TCGGCAACGCCCTGATGCAG                         GACCCCGCAATNTCNGNCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: TCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162156693|gb|FC333549.1|FC333549
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208360463|gb|DC930816.1|DC930816
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162174547|gb|FC350202.1|FC350202
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162210973|gb|FC387071.1|FC387071
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162155861|gb|FC332410.1|FC332410
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162209197|gb|FC385416.1|FC385416
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162151736|gb|FC328593.1|FC328593
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162192827|gb|FC369652.1|FC369652
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208386947|gb|DC956930.1|DC956930
EST:     TCGGCAACGCCCTGATGCAG                         GACCCCGCNATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: TCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162187054|gb|FC362836.1|FC362836
EST:     AGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: AGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162277694|gb|FC453533.1|FC453533
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162153901|gb|FC329408.1|FC329408
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162182198|gb|FC358213.1|FC358213
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162176549|gb|FC353018.1|FC353018
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162247198|gb|FC420240.1|FC420240
EST:     AACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: AACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100388693|gb|BY970841.1|BY970841
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162189806|gb|FC366055.1|FC366055
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100390591|gb|BY971346.1|BY971346
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162152256|gb|FC328235.1|FC328235
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162157916|gb|FC334902.1|FC334902
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG

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), 33 (downstream exon)
Score: 79

CCAGTTGGACCCGAACCAGTACATCAACGCGATGCAACAAGTGATGCAAAATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAGGAGCAGCTGGAGCAGCGCATGGCAGCGGTACGAGAGGATCCGACCCTGA




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