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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA

Basic information

species Physcomitrella patens
transcript PP1S39_197V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
-----------------------ctt--tctcatcgtaactttttgtatgtactgaatgtagca---gtgacgagattagtactattgt-tgcctacgataacctggtaatcatcacct-gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
                       |||  | |  ||| |   | |    ||   || || || ||   ||  |  ||    |  | |    |  |||  ||   ||| | |  | |   | |   |||||| || ||||| ||||||||||||| ||||||||| |||| |||||||||||||  ||||  || ||  | |        |||||  | ||  | |||||||
gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatt-tctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G002616_T01 (Zea mays), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcat-cacctgtgg---atgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
        |    | || |  | | |    ||  || |  ||    |   |   ||  |     |  |    ||||  || || | || ||||      |  || |||||||||||||||| || ||||| ||  | ||||| ||||||||||| ||||||||||| ||| |  |   |||||| | ||| ||||| ||||| |
-------gtaagcaattctattttatcagaaagataactttgttttgcacatctctccttaacacgtcctccaccttatattctttcaactgtcctttgtttagCTGCTGGCTATGATTGGTGAACAATTCGACTATGGTGATGAAATTTGTGGCGCAGTTGTCAGTGTGCGTGGGAAGCAGGAAAGAATTGCTATTTGGACAA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G113096_T01 (Zea mays), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtact-attgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
          ||    |||| |  | |  |   ||     |   || ||  || || ||| | |||| |  |   |      |   |||   |   || || || |||||||||| || || ||||| ||  | ||||| ||||||||||||||||| ||||||||| |  |   |||||| | ||||||||||||||| |
---gtaagcagttttattttatcagaaaagggagttttgttcttgacatctgtccttattatagcctccagtcctccacccttacacactgtttcttgtagCTGTTGGCTATGATCGGCGAACAATTCGACTATGGTGATGAAATTTGTGGAGCAGTAGTCAGCGTGCGTAGCAAGCAGGAAAGAATAGCTATCTGGACAA

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 2
------ctttctcatcgtaactttttgtatgtactgaatgtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctgtgg-atgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCG-CAGGACAAAATA-GCTATCTGGACTA
      | |||| | | ||||  |     | ||||        | |||    | |   |  |||   ||  |  | | ||  | |    ||  | | ||  ||| ||||| ||||| ||||||||||||||||||||||||  || || |||||||| |  ||||  || ||  | | |  | |    ||| | | ||| ||       
gtattacattctaaccctaaccctaaccttttact-----cttctgtgttttgttagatgatatg--tggttttggtgactggtt--ctatttcttatgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGTGTGGTTGCTAGTGTCCGTCCACAGTCGAAGCAAGACAAGCTCTCCTTGT--

upper sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G18040.1 (Arabidopsis thaliana), 3'ss of exon 2
ctttctcatcgtaactttttgtatgtactgaat-gtagcagtgacgagattagtactattgttgcctacgataacctggtaatcatcacctg-tggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
   |    |    | | ||  | | |  ||| | ||| |     ||  || | | | ||||   |  ||       |  |  |  | || || | | |  ||||||| ||  ||||||||||||| |||||| | || || ||||| |||||||||||||||| | | ||| ||  ||| || |  ||| |||| |||||||
--gtacggtttctattcttcttttattttgactcgtaactcctgcgtcatca-tccaattgaatctcac--cggttt--ttctttttacatgcttggtttagTTGCTTGCATTGATTGGAGAGCAGTTTGATCATGGAGATGAAATATGTGGAGCAGTTGTCAACATTAGAGGAAAGCAAGAAAGGATATCTATTTGGACTA

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|208369044|gb|DC931290.1|DC931290
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67571986|gb|BJ944810.1|BJ944810
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|208374804|gb|DC932059.1|DC932059
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67712745|gb|BJ966194.1|BJ966194
EST:     CACCCAGGAGCGGCGGCNAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGA
EST: gi|208370617|gb|DC936133.1|DC936133
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67507600|gb|BJ940481.1|BJ940481
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|19788032|gb|BQ040702.1|BQ040702
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGA
EST: gi|100394449|gb|BY972074.1|BY972074
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67569897|gb|BJ942721.1|BJ942721
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGA
EST: gi|162225236|gb|FC402002.1|FC402002
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
EST: gi|67576793|gb|BJ949617.1|BJ949617
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACG
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACG
EST: gi|208374770|gb|DC932039.1|DC932039
EST:     CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACA                         TTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA
genomic: CACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGA

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: 18

TAAATGGGAGGACCCTAAGTGTGCCCATGGTGGCAAATGGACTGCTCAGCCACCCAGGAGCGGCGGCAAGGCTGTGCTTGACACCTACTGGCTTCACACAgtattgtcca ... gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattagtactattgttgcctacgataacctggtaatcatcacctgtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA
                      cgataac  putative branch site (score: 18)
       tactatt  TA-rich tract