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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

Basic information

species Physcomitrella patens
transcript PP1S301_53V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
---atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagt---tgttttgtatcgt----ttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
   ||  | | | |||||   | |        || |   |||    ||| || |   |     |   | || | |||      |   ||| |||  || |     ||||||| |  |||||||| |||||||| || ||||| || ||||||||||| ||||  || || |||||  |||| ||||| |||||||| |||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
---atcttattcgtgttatttttatctggtattattggcttggtattcaa-gatccgcaggtgctgggaatgta-ctaatataagttgttttgtatc---gtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
   || |  | | |||||   | |     |  |  |  ||| ||   ||| ||   |||  |  |     || | | ||  | |    | |  ||        ||||| | |  |||||||| ||||||||||| ||||||||||| |||||||||||||  ||||| |||||  |  | ||||| ||||||||||||||
gtaatttcttccatgttaagataaataattgatggtt-ctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
         |   |  | | | |||  || |||     || |   |   |            | |||||| |  ||| |  |       |    || ||||| |  ||| | ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||  | ||||| || |||||||| ||  |
-------gtgaaattctctcaactga-ataattaaaaaggaagctat--ttgatgaacaaaagtaatgtaattttatgatat------cactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
---atcttattcgtgtta----tttttatctggt-attattggcttggtattcaagatccgcaggt--gctgggaatgtactaat--ataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
   || |  | | |||||    |   ||  || | ||| || |      || ||  |  |  |  |  |||||      ||| ||  ||  |||  || | |     ||||| | |  |||||||| ||||||||||| ||||| ||||| |||||||||||||  ||||| |||||  |  | ||||| ||||||||||||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaac----tgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
atcttattcgtgttatttttatctggtattattggc--ttggtattcaagatccgcaggtgc-tgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
           ||||  ||    || |  |||  |   |  | | | ||   | || | |   |       || |||  |   |  |||| | | |    |||||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | |||||||| |||||
-----------gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaac-tggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgc-tgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
                 ||    |   ||  |||| |  | | | ||  || || | |   |     | || |||  |   |  |||| | | |    |||||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | ||||| || |||||
----------------gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaac-tggctcttttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
atcttattcgtgttatttt-tatctggt--attattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
 |   |||| |||  ||   ||  || |  |||||    ||  |  |   | |  |  |  | |   | ||      ||||  || | ||  | | |   ||||||| ||||||||| ||||||||||| || || || ||||| || |||||||| ||||| |||||  ||||  |||| |||||||| |||||
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcga-gttataactg----gttatattttatgtttgaacatgc-cagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
      |  | | | | ||| | ||| ||  ||   ||| |      ||| |    ||| ||  |    || |   ||   ||||||    || |||||||| | |||| |||| ||||||||||| || || || || |||||||||||||| |||||||||||  || | ||||| || ||||| |||||
-----gtgagagct-tctttctgtggcatcttttatttgtt------gattct---gtgttgaaagctaaccacgtta---tgttttac-ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------atcttattcgtgttatttttatctgg-tattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
                            || ||  || |  ||| || ||  |    ||   ||||  || |   ||      |       || || | ||     || |||   ||| |   ||||| |  |||||||| |||||||| ||||| |||||||| |||||||||||||| ||||| |||||  | || || || ||||||||||||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaa-atcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagt-----tgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
       |    ||  |||  || |  |    |  |   | |  |||  ||  ||  | ||       | ||||| | |       | | ||   |  | | ||| | |  |||||||| |||||||| || || || || || ||||| |||||||| ||||| ||||| |||||||||||||| ||||| |||||
------gtgagcttgctttcctcagaaaagtcttacacagaa--caacttctacat-tactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
-----atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatata-----------------agttgttttgt-atcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
     || || ||| | | |  | ||||      ||  |||    ||  |||  |    |  || |   | ||||  | | ||                 | ||||  | | ||| |   ||| | | |||||| || |||||||| || || || |||||||||||||||||||| ||||| ||||| |  || || || |||||||| |||||
gtgcgattttcttcttttgaaatctatcat---ctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

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|37828516|gb|BJ586528.1|BJ586528
EST:     AATCTGTCCCCGTGGCTACGTTCAAAGTTCACGAGCATTTGCGACCAAAG                         CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGT
genomic: AATCTGTCCCCGTGGCTACGTTCAAAGTTCACGAGCATTTGCGACCAAAGgtaatcttgg ... tcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGT
EST: gi|37826792|gb|BJ584804.1|BJ584804
EST:     AATCTGTCCCCGTGGCTACGTTCAAAGTTCACGAGCATTTGCGACCAAAG                         CTTTACGATTTATACGAAAATGACTCTATTTTCGGCAAGTTTGAGTGTTGT
genomic: AATCTGTCCCCGTGGCTACGTTCAAAGTTCACGAGCATTTGCGACCAAAGgtaatcttgg ... tcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGT

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), 9 (downstream exon)
Score: 2

CTGTGGGACGTCAACATGGAATCTGTCCCCGTGGCTACGTTCAAAGTTCACGAGCATTTGCGACCAAAGgtaatcttgg ... tcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
                       tactaat  putative branch site (score: 2)
                          taatataagttgtttt  TA-rich tract