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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggtagggtagggagtggttggagcagcgtgggtgcgtggcagtgtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA

Basic information

species Physcomitrella patens
transcript PP1S77_16V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_16V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G116034_T01 (Zea mays), 3'ss of exon 4
---gtggtagggtagggagtggttggagcagcgtgggt-gcgtggcagtgtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA
       |    |         | | ||||   ||    ||    || |    | |||    |||    |   || |||    |      | | |||  ||||||||||||||||||||||||| || ||    ||| |||| || || || ||||| || ||||||||||| || ||||| ||||| ||  | ||||||||||
tctacacttcttttatcttctatcgcagcaatctgaaaagcaaaccatttatcttactctaattgatttat--gcctactgacttt--ctttcgtgaaatgcagATTTACGACATCTTCCAGCTTCTCCCAGCCAAGATTCAGGTTGGAGTCTTCTCTGCTACCATGCCCCCTGAGGCCCTTGAGATTACCCGCAAGTTCATGA

upper sequence: PP1S77_16V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
gtggtagggtagggagtggttggagcagcgtgggtgcgtggcagtgtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA
           |   |    |    |   |||  |   |  || | |||| |  | | ||  ||  |   || ||  | | | | ||   |      ||||| || ||||| |||||||| || || |  ||| | ||||| || ||||||||||| || ||||| || ||||| || |||||||| |||||||||||||
-----------gtatgcaaatatttctcagtgtttcaattccattctcgtta--tagttta-acttgaatctcactggtttctgggtttttt-----cagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA

upper sequence: PP1S77_16V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16567 (Selaginella moellendorffii), 3'ss of exon 3
gtggtagggtagggagtggttggagcagcgtgggtgcgtggcagtgtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA
                                   |   ||  |    |  |  |||  |  |  |    | | |||| |||  |||   |     |||||||||||||||||||||||| || |||   ||| | || |||||| | ||||||||||| ||||| || || || || ||||||||  | ||||||||||
-----------------------------------gtaaggtggaag-gaaagctggtctatataaccaccctgcctg-tgccttgtgtgt----cgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTCTCCGCCACAATGCCGCCCGAGGCGCTGGAGATCACCCGCAAGTTCATGA

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|208372422|gb|DC936510.1|DC936510
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCANGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162276618|gb|FC452196.1|FC452196
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162245915|gb|FC420504.1|FC420504
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|100403338|gb|BY991153.1|BY991153
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|67718867|gb|BJ969126.1|BJ969126
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|208363851|gb|DC943308.1|DC943308
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162216576|gb|FC392473.1|FC392473
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|208373838|gb|DC956326.1|DC956326
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGG-TTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|100447722|gb|CJ972021.1|CJ972021
EST:     TCGTGCTGGACGANGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCC-AGAN-CTTCANGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162253751|gb|FC429865.1|FC429865
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|100366885|gb|BY948259.1|BY948259
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAGGGAC-AG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTTCA-GTGGGCGTGTT
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTT-CAAGTGGGCGTGTT
EST: gi|67719143|gb|BJ969402.1|BJ969402
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCC
EST: gi|208361430|gb|DC930399.1|DC930399
EST:     TCGTGCTGGACGANGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACAAG                         ATTTACGACATCTTCCAGCTGCTGCCC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCC
EST: gi|100446207|gb|CJ970506.1|CJ970506
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGNACCAG                         ATTTACGACATCTNCCAGCTGCTGCCC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCC
EST: gi|100381333|gb|BY950077.1|BY950077
EST:     CGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTTCAGGGAC-AG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTTCA-GTGGGCGTGT
genomic: CGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTT-CAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTT-CAAGTGGGCGTGT
EST: gi|100370659|gb|BY948453.1|BY948453
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTTCA-GTGGGCGTGTT
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTT-CAAGTGGGCGTGTT
EST: gi|162156058|gb|FC332225.1|FC332225
EST:     GACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: GACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162164223|gb|FC342038.1|FC342038
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|162187052|gb|FC362834.1|FC362834
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|100394790|gb|BY989926.1|BY989926
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|100409310|gb|BY991947.1|BY991947
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|67724165|gb|BJ974424.1|BJ974424
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|67719407|gb|BJ969666.1|BJ969666
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCGAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCC
EST: gi|162177225|gb|FC352654.1|FC352654
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTC
EST: gi|67719277|gb|BJ969536.1|BJ969536
EST:     TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTGCTGCCCCA-AAGCTTCA
genomic: TCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCA

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), 31 (downstream exon)
Score: 42

GTACGACATGTTGCGCAGGAATGCGCTGCGCGCGGATTCCATCAAGTGCTTCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgtt ... tgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA
                       ggcttac  putative branch site (score: 42)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtagggtagggagtggttggagcagcgtgggtgcgtggcagtgtcgtgacttggcttggacgagtggcttacctggtgcggtgtccatgacgtgcagATTTACGACATCTTCCAGCTGCTGCCCCAGAAGCTTCAAGTGGGCGTGTTCTCCGCCACCATGCCCCCGGAAGCCCTCGAGATCACGAGGAAGTTCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA