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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgcaaatttctccgcaagccaatgacttctcaattcttaattaattatatatctcatcacagttttattaacttccaaatttatctatcggtgg...

Basic information

species Physcomitrella patens
transcript PP1S126_38V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA14G40320.4 (Glycine max), 5'ss of exon 3
GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgcaaatttctccgcaagccaat---------gacttctcaattcttaattaattatatatctcatcaca-gttttattaacttcca--aatttatctatcggtgg
||||||||| ||||| ||  || | ||||||||||||||| | ||| | || || ||||| || ||||||||  | || ||||| ||||||||||||||||||||       ||| |    ||   | |          | | ||    | | ||||  |||| |   |  |   | | ||| ||||   | |  ||| |    ||    | 
GTTCCAAGCGGAAGTGTCGCGGCTTATGGATATCATCATCAATTCTCTCTACAGTAACAAGGATATCTTCCTCAGAGAGTTGATTTCCAATGCTTCTGATgtaagcgctttttttttaaaaaaaatatttttgtttaaaaatccttgcatttaaattttttatttgaattgttgaacgatttgttaatggcgaataatgtgcacattctag-

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 3
-GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagt-tgcaaatttctccgcaagccaatgacttctcaattcttaattaattatatatctcatcacagttttattaacttccaaatttatctatcggtgg-------------------------------------------------
 ||||||||| ||||| ||| || | |||||||| |||||| | ||| | || || ||||| || ||||||||  | || ||||| ||||||||||||||||||||  |     |||    |  |   | |    |   ||     |  || | ||||   |  | ||| ||||   ||       |||||  | |   |                                                   
AGTTCCAAGCGGAAGTGTCACGGCTTATGGATATTATCATCAATTCTCTCTACAGTAACAAGGATATCTTCCTCAGAGAGTTGATTTCCAATGCTTCTGAtgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttaca-ttttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattcta

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 3
GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgcaaatttctccgcaagccaatgacttctca--attcttaattaattatat-atctcatca----cagttttattaacttccaaatttatctatcggtgg
|||||||||||| || ||  || | ||||| || || ||| ||||| | || || ||||| ||||| ||| |  | || ||||||||||||||||||||||||||  ||    |   |        | ||| || |    || | |  |||| ||    | || || |    | || ||  | | || ||                 
GTTCCAAGCTGAGGTTTCTCGGCTTATGGACATTATTATCAACTCTCTATACAGTAACAAGGACATTTTCTTAAGAGAGTTGATCTCCAATGCTTCTGATgtaagcagcttcgtgtacattgttttagtgagtttttgggatacctcgttaaataggggaactaataagtgtctgtgttggtgattttcag----------------

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 3
GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgcaaatttctccgcaagccaatgacttctcaattcttaattaattatatatctcatcacagttttattaacttccaaatttatctatcggtgg
||| || ||||| || ||  || | ||||||||||| ||| ||||| | ||||||||||||||||| ||| |  | || |||||||||||||||||||||||||||    | ||| |  |    | |   ||||     |||| || |  |||  ||    ||   | || |  |   || ||                 
GTTTCAGGCTGAGGTGTCTCGGCTCATGGATATCATTATCAACTCTCTTTATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagt-attattttgtttgttt-ctaggaactttct--ttctgaagttgttactta----atggtaattctgcttgatttcag----------------

upper sequence: PP1S126_38V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ28825 (Selaginella moellendorffii), 5'ss of exon 3
GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca-aatttctccgcaagccaatgacttctcaattcttaattaattatatatctcatcacagttttattaacttccaaatttatctatcggtgg
|||||| |||||||| || ||||||||||| || ||  || ||||| | ||||||||||| || ||||||||||| ||  | || || || || ||||| || |||   |   ||  |  |     |   |  |   |   ||||  ||  |  | | | |  ||||||                                
GTTCCAGGCTGAAGTTTCGAGGTTGATGGACATTATTGTCAACTCTCTATATAGCAACAAGGATATCTTCCTTCGAGAGCTTATTTCGAACGCCTCTGACgtgagtgagatggttgatttggtgttcgccgtttgagcccctcttc-ttcttgttcttttttctcacag--------------------------------

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|18367288|gb|BJ199370.1|BJ199370
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18372090|gb|BJ203692.1|BJ203692
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGAATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGA-TTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
EST: gi|18346979|gb|BJ179025.1|BJ179025
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18346023|gb|BJ178066.1|BJ178066
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18354827|gb|BJ186886.1|BJ186886
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18357801|gb|BJ189860.1|BJ189860
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18329083|gb|BJ161089.1|BJ161089
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18343471|gb|BJ175509.1|BJ175509
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18331239|gb|BJ163248.1|BJ163248
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18332430|gb|BJ164443.1|BJ164443
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18344948|gb|BJ176989.1|BJ176989
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18375456|gb|BJ207034.1|BJ207034
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGNATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAG-ATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
EST: gi|18347429|gb|BJ179475.1|BJ179475
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|100406123|gb|BY991551.1|BY991551
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18360762|gb|BJ192825.1|BJ192825
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18364379|gb|BJ196452.1|BJ196452
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGAATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGA-TTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGG
EST: gi|18327014|gb|BJ159015.1|BJ159015
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGA
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGA
EST: gi|67719606|gb|BJ969865.1|BJ969865
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
EST: gi|18343482|gb|BJ175520.1|BJ175520
EST:     ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGAT                         GCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC
genomic: ATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGC

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: 38

GTTCCAAGCTGAAGTCTCAAGGTTGATGGATATCATCATCCACTCTTTGTATAGCAACAAAGACATCTTCCTTCGCGAATTGATCTCCAATGCTTCTGATgtaagttgca ... gagtacgcagGCGTTGGACAAGATTCGGTTCCTTTCTCTCACCGATTCTTCAGTTCTTGGCGAAGGAGATGACGCAAAACTGGATATCCAC




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