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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA

Basic information

species Physcomitrella patens
transcript PP1S425_2V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
--------ttat-ttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
        |||  || ||||| | |  |  | |||||       ||| | || ||  |  | |||  ||||  |||  | |   |||  |  |   ||||       ||||||||||| | || |||||||||||||||||||||||||| || || || ||||||||||| ||||||    | |  |  || || ||||| |||||||
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcac--atctatgtttttttgatgaactgttct-------agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||  |  | ||||  | |  ||  ||| |  ||  |   | ||      |    ||  | |   | |  | |||| |  || ||| |||||||| ||  | |||||||||||||| || ||||| ||||| ||||| ||||||||||| |  || ||||  || |  || || |||||||| |||||||
-----------gtaatcatcatttggtcagtaatgttgcaccaacatcc-tatgggtcagaagagtcaatatt--tataatgtatgatcattgttt-cagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactt-tcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||  |||| | |   ||   ||   ||    || |     |||  |  ||   || |||  || || |   || || || || ||| |||||||| ||  | ||||||||||||||||| ||||| || || ||||| | ||||||||| || |||||||  |||  ||| || || || || |||||||
-----------gtaattttcagtcactggttaatgctgcctgaaat---gcttgtggagcagaaat-gttaacatttatgacatgtgattgttgttt-cagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
 |||||| | |  | | ||   || ||            |   ||||   | |    || |    || ||||||   ||   ||| ||| ||     |||||||||||| | ||||||||||| ||||||||||| || || |||||||||||||| || || || ||||  ||||  ||||| || || ||||||||||
gtatttgatttactctgttttcttctta--------ctcagctatttggctataccttttatctgtc-ttttcatgctc---tatccttgtttac--cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||   ||  |  || | |  | | ||    ||    |||||    ||||  ||| |   |  |    | |   |     |   || |||||||| ||  | ||||||||||| ||||||||||| ||||| ||||| |||||||| ||| | || ||||  ||   |||||| |||||||| || ||||
-----------gtacattaaaacttatcaccagatttcacttacgagtaatt--gtgttccttgagctactcaataagcttgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
 |||||  | |  ||| ||| |        ||  |||||| |  |      ||    ||   |  || |  | | | | |  ||| | | |  ||| |||||||||||  | ||||||||||||||||||||||| |||||||| ||||||||||| || || || ||    ||   |||||| || || |||||||| |
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttt--tcttactaaatctagactattcgt-tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
---------ttatttgttgtgttgttttga---ttttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
         | ||  |||         |||   || |||| |  |   | |  | | |    | |||| |    | || | |  ||| || |  ||| ||   |  |  |||||||| ||  | ||||| ||||||||||||||||| |||||||| || |||||||||||||| || ||||  || | |||||| || ||||| |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacatt-gcttattctctgtgct--cagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
----ttatttgttgtgttgttt-tgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttc--actttcgtatatgcttcttc----------tttg----cagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
       ||     | | |||| ||  ||  |||  |  |   || |  |||||  |||    ||    ||| ||     ||| | | || |  |||| |          ||||    |||||||| ||  | ||||| |||||||| |||||||| ||||| || ||||||||||| ||||| || ||   ||| | |||||| || || || |||||||
gtgtcctttaagaatttcgtttctgggttgctgatgattaccata-tccttttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

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|162150295|gb|FC326380.1|FC326380
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
EST: gi|100389123|gb|BY952327.1|BY952327
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTT
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTT
EST: gi|162255330|gb|FC432056.1|FC432056
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
EST: gi|100386449|gb|BY951245.1|BY951245
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTT-ATTACTTTAAGAGTTTGGAAATA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATA

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: 33 (upstream exon), 35 (downstream exon)
Score: 8

CAAAGGACACGAAGGGAGTTGGAAAAGGCTAATACTGTGGTATCGAGGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
              cactgat  putative branch site (score: 8)
                                     tatgcttcttcttt  putative PPT
                                   tatat  TA-rich tract