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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgagttgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag

Basic information

species Physcomitrella patens
transcript PP1S201_25V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA05G29080.7 (Glycine max), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgagttgaggttttggatgcc--tgtggg--acgtgcttttcttttggcggggttcgt----aactgactgtgcgattgactgcgtggtggtag-----------------
 ||| || | | | || || ||  | || ||||| || ||  |||| ||||| ||||||||||||||||| |||||||| ||||||||||| |||||  |||| || ||| | || |  ||   ||      | | |   |  |||    || || | |   |  ||    || |   ||   | || ||    |      ||                 
CTACTGCCGAGGCTGAGTTAGCATCCACACATCCCATCCGTTTGGGCCTGGCTTTGAACTTCTCTGTCTTTTATTATGAAATTTTGAACTCTCCTGAAAGgtatgacttttattttattttcctgacagtattattgtttaattgcccacctcttcgtgtactatgtgccaaagttggtgcctgcttaacaaatttaacacagtactcttcatgtctcag

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA08G12220.5 (Glycine max), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgagttgaggttttgg-----atgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag----------------------
 ||| |||| | | || ||  | || || ||||| || ||  |||| ||||| ||||||||||||||||| |||||||| ||||||||||| |||||  |||| || ||| | || |  ||   |     ||  ||||   |  |||    || || | |   |  ||  || | | || |      |         ||                       
CTACTGCAGAGGCTGAGTTACCACCCACACATCCCATCCGTTTGGGCCTGGCTTTGAACTTCTCTGTCTTTTATTATGAAATTTTGAACTCTCCTGAAAGgtatgacttttattttattttcctgacagtattactgtttaa-atgccaacctctttgtgtactatgtgcctaagt-tgggccctgtttaacaaatttaacaccatactcttcatatctcag

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA13G36690.1 (Glycine max), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgagttgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag
 | |||||| | | || ||  | || || ||||| || ||  |||| || || || || |||||||| |||||||||||||| ||||||||||||||  |||    || ||  ||    |  |         |||    || || |   || |    ||   ||| |    |||   ||   | | |  |   ||
CTGCAGCAGAGGCTGATTTACCTCCCACACATCCCATCCGATTGGGTCTAGCTTTAAATTTCTCTGTTTTCTATTATGAGATCTTGAACTCCCCTGAAAGgt----ttgtggcttttattccta-----tcctggattatgattgttgattagtattgtgtttaa-tatgggtgattttattttcctatttccag

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA07G35240.1 (Glycine max), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgag-ttgaggt---tttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag---
 ||| |||   |||||  |  |  |||| ||||| || || || ||||| ||  | |||||||| |||||||||||||||||  ||||||| |||||  ||||   ||||    ||  |||   ||           |  | |  |  |        |    || |  | | | | |    |    |||    |||      
CTACTGCAAGCACAGATCTTCCATCAACACATCCAATCCGTCTTGGACTTGCACTCAACTTCTCAGTCTTCTATTATGAGATACTGAACTCTCCTGAAAGgtattttttttttcttttggtccattcaagcattgccgcaaagaaccataaaaacaacaaactttg--agttattttattctctgttgccatttggggcctt

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA20G03120.1 (Glycine max), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagattttgagttgaggttttggat--gcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag----
 |||||||   |||||  |  |  |||| ||||| || || || ||||| ||  | |||||||| |||||||||||||||||  ||||||| |||||  |||||  ||||   ||    ||||   |  | |  |   | |     ||     ||          |||  ||| |    ||   |   |    || |    
CTACAGCAAGCACAGAGCTTCCATCAACACATCCAATCCGTCTTGGACTTGCGCTCAACTTCTCAGTCTTCTATTATGAGATACTGAACTCTCCTGAAAGgtaattttttctattttttttttctcttggtccatacaa-gcatagttgcaaaggatcataaaacaacaaactttcaagttattttattctctgttgcaat

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv10s0003g01240.t01 (Vitis vinifera), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaa---------gattttgagttgaggttttgga----tgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtggtag
  ||||||| | | || ||  | || || ||||| ||||| |||||  ||||||||||||||||||| || || ||||| ||| |||||||||||||  ||||           || || ||   | ||| || |    | ||| |     ||  |||  ||||       || | |||||  |    | |    |   |    |   
CGACAGCAGAGGCTGATTTATCTCCCACACATCCCATTCGACTGGGTTTGGCCTTGAACTTCTCTGTTTTTTACTATGAAATTATGAACTCCCCTGAAAGgtattcctatcgtaatcttcagagaaagttctgtaatagtcccttttttgtgtcttttgattttttgtccatttgaaactgtttacatggtaacttatttcccag---

upper sequence: PP1S201_25V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0001g05720.t01 (Vitis vinifera), 5'ss of exon 4
ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgt-----aagattttgagttgaggttttggatgcctgtgggacgtgcttttcttttg--------gcggggttc--gtaactgactgtgcgattgactgcgtggtggtag-------------------------------
 |||||| |   ||||  || |||| |||||||| ||  | || || ||||| |||||||| ||||||||||| ||||| |||||||||||||| ||| |||     | | | |    ||  |  | |  ||   | |||    |  | |  | ||          ||| | ||  |    |     | |  ||   || || ||    |                               
GTACAGCTGCCTCAGATCTGCCGCCTACTCATCCAATCAGACTTGGGCTGGCTTTGAACTTTTCTGTCTTCTACTATGAAATTTTGAACTCCCCAGAGAGgttgatcatgctctctgatttggactatttatttttttggtttcttttgtgttcttacatcaagaacggaggtctagaggtttttcctccactttcttgagttgttaaggttctgttttgttttaaatttgtgttgcacag

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|162205866|gb|FC381104.1|FC381104
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAAGCA-GCATTCGACGAGGCAATTGCCGAATTGG
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAA-GCAAGCATTCGACGAGGCAATTGCCGAATTGG
EST: gi|208397825|gb|DC916160.1|DC916160
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|162232156|gb|FC408031.1|FC408031
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|162276326|gb|FC452628.1|FC452628
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208352969|gb|DC913853.1|DC913853
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGANCTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCANGCAT-CGACGAGGCA-TTGCCNA-TTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|162228076|gb|FC404644.1|FC404644
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208379881|gb|DC927607.1|DC927607
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208396625|gb|DC924293.1|DC924293
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCNTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|162252871|gb|FC429244.1|FC429244
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|67694367|gb|BJ954600.1|BJ954600
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208365604|gb|DC944102.1|DC944102
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208348120|gb|DC916930.1|DC916930
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTTGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|162228075|gb|FC404643.1|FC404643
EST:     GCCTTGAACTTCTCTGTCTTCTATTAGGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|208376281|gb|DC940979.1|DC940979
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAANCA-GCATTCGACGANGCANT-GCCGANT-GGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
EST: gi|67694695|gb|BJ954928.1|BJ954928
EST:     GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCG                         GGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA
genomic: GCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGA

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), 35 (downstream exon)
Score: 106

ATACAGCAGTGACAGACTTGGCGCCAACTCATCCGATTCGGCTGGGACTGGCCTTGAACTTCTCTGTCTTCTATTATGAGATTTTGAACTCCCCTGAGCGgtaagatttt ... gtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA




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