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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgggttatgtcaatgtgtggcaacgttggcgcttctattgcc...

Basic information

species Physcomitrella patens
transcript PP1S137_144V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaaga---cgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgggttat--gtcaatgtgtggcaacgttggcgcttctattgcc
    || ||||| || ||||||||||| || |||||||||||||||||||| ||||| |||||  | || || |||||||| ||||| || ||| ||||||||| |     | |||  |  ||    ||  | | |    |    | |||     ||  | ||   | |  |    ||| |  |         ||||  |     
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa-----

upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 5'ss of exon 3
GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcct-ttgcaaatgtttgctgattttcatgtgggtgtgaaacgc--aatgccaatgggttatgtc-aatgtgtggcaacgttggcgcttctattgcc
|   || || || || ||||||||||||||||| || || || ||||| || || ||||||||  || |||| || ||||| |||||||| |||||||||||||   || | |||| ||  ||   || | ||||| ||  |   |    |   |    ||  |   ||||   |    |    |  |   |   | | |    
GATCTCAGCAGTAGCAATTAAGAATGTGACTATAAACGATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgcttattgccaaacttca-tgttcttcatttgaattcaatttactagaaaataacagaaaatgtttgaaaaataaagaactcaacatatttgtg---

upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 5'ss of exon 3
GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgg-gttatgtcaatgtgtggcaacgttggcgcttctattgcc-
    || ||||||||||| |||||||| || || ||||| || ||||| || || || || ||| || |||| || ||||| ||||| || |||||||||||||    | | | |   |   |  | | | |  | |     | |   ||| |     |   ||||  |  ||| | |  || |||  |  || |  | |  
AGTTTCTGCTGTTGCCATAAAGAATGTAACAATAAATGATAACTTCTTTCCTGGGCATTTTCCCGAGAGGCCAATTATGCCTGGTGTTCTCATGGTTGAGgtaattt-cttgttcccgtaccttttaaatatttttttttctttagttgcattatttttaaagttacatgtatgag-gtaaatgtttccatttttgctacaa

upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP03190 (Chlamydomonas reinhardtii), 5'ss of exon 2
-----------------GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgggttatgtcaatgtgtggcaacgttggcgcttctattgcc
                 | |||  ||||| | |   |||  ||| || || || ||||| |||||||| |||||||||||| |||| || |||||||| |||| |    |  |||   | ||  ||   |      || ||     |  |  ||| |   | |||    ||   |   | ||   |  |||  | | || |                
GTTGAGTGGGAGAAGGAGAAGTACGCTGTGGGCTACAAGTGTGTCACCATTAACGACAACTTCTTCCCAGGCCACTTCCCCGAGCGCCCTATCATGCCTGgtgagtgacttcttggcatcagcagcgact-----cgtctgggccatggcg-gtgcgcacgcaactagctgtacagatgctacagcgctgtcagcctacttgaatt-----------

upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
-GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgta--agacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgca-atgccaatgggt--tatgtcaatgtgtggcaacgttggcgcttctattgcc
 |    |||| || |  ||||| || ||||| |||||||||||||||||||| |||||||| ||  || | || |||||||| || || || ||||||||||||  | |||      || |   ||     || |   || | | | | |||   ||||   |   |  | |||| |                             
TGTCA-CGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaatt-----ttcttgcgtagttctaatacgttcatgcttttaaatcttctgtccag----------------------------

upper sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ06529 (Selaginella moellendorffii), 5'ss of exon 3
-GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgggttatgtcaatgtgtggcaacgttggcgcttctattgcc
 |    |||| || |  ||||| || ||||| |||||||||||||||||||| |||||||| ||  || | || |||||||| || || || ||||||||||||  |  |  |   | |     |   |||||| || |    |   | ||  |   |||   || |||| |                             
TGTCA-CGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagaca-----gagaattttcttgcgtagttctcatgcttttgaaat---ttctgtccag----------------------------

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|162272078|gb|FC447872.1|FC447872
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|67691492|gb|BJ951725.1|BJ951725
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|208368931|gb|DC947489.1|DC947489
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|37849594|gb|BJ607602.1|BJ607602
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|162272079|gb|FC447873.1|FC447873
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|37838699|gb|BJ596707.1|BJ596707
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|37821509|gb|BJ579575.1|BJ579575
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|162262212|gb|FC437123.1|FC437123
EST:     ACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: ACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|208373527|gb|DC941096.1|DC941096
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAAGAAGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|208366611|gb|DC955645.1|DC955645
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|162262213|gb|FC437124.1|FC437124
EST:     ACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: ACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
EST: gi|67508275|gb|BJ941144.1|BJ941144
EST:     CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAG                         GCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC
genomic: CGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGC

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), 30 (downstream exon)
Score: 14

GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaagacgcc ... gtgagtatagGCTATGGCGCAAGTAGGAGGTATCGTGATGTTGCAACCTGATGTGGGGGGCTCAAAGGAGACTTTCTTCTTCGCTGGAGTGGACAAAGTGCGCTTCCGGA




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