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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctttctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca...

Basic information

species Physcomitrella patens
transcript PP1S204_49V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 1
-CTGAGCCCCAGCCAGC-AGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcct---cctttctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca
      || ||  ||   | | | |  |  ||||| ||||||||    ||  | || || || |||||||||||||||||||| ||  ||||||||||||| || ||   || |  ||    | ||| |||||     | |   | ||||        | || | | | || |   |     ||| ||    |   |  || |  
GGCACACCTCACTCACTGAACGGTA--AGTATGGCGGACAAGGCTGTTACAATCCGAACCCGAAAGTTCATGACCAACAGGCTTCTTTCCAGGAAGCAGTTTgtgagtttccctttcccttccttttttcgctacaaatct---gcacataattactcgaaatatcactttcggagtcctatttgattactttcaagctttgttt

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA03G40530.1 (Glycine max), 5'ss of exon 1
CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctt-----tctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca
   ||| |   |   | | |     |  ||||| ||||||||    ||  | || || || |||||||||||||||||||| ||  ||||||||||||| || ||   || |    ||  |     ||||            || || ||    ||      ||    ||| || | ||    || || || || | | ||| | 
TACAGCTCACACACACTGAACGGTAAGTATGGCGGACAAGGCTGTTACAATCCGAACCCGAAAGTTCATGACCAACAGGCTTCTTTCCAGGAAGCAGTTTgtgagtttcccttttttctctacaaatctccacctaataacttgaaatatcactttcccagtcat---atttgattatttttctgctt-tgttttttaattcgc-

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGAGCCCCAGCCAGCAGCAGCAGCATCA-TGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctttctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca-------
 | |     | ||   || || ||||  | ||||||| ||||||  |||  | || ||  | || |||||||||||||| || ||| |||||||||||||||| ||   || |    |  ||||||   |    | |    | ||||   ||||    |  ||   |   |||||     |  | | ||| | | ||   |       
-TCACTTTAATCCTTGAGAAGTAGCAAAAATGGCTGAAAAGGCGGTCACCATCCGAACCAGGAAATTCATGACCAACAGACTTCTCTCCAGGAAGCAGTTCgtgagt-tccattattttttttctcttctcta-tctgcatatcatt--tttgtt---cttctgggttttgttttaatgggaatctagttataatttgatatgaaccc

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 1
--CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctttctcgcttagggtttctggaacattggctt--gtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca
  |||| | |        |   |||||  |||||| || || ||   |||| |  | ||  | || ||||||||||||||||| |||||||| ||||| ||||| ||  ||| |  |    || |    |      |    |      | |||   |||| |   | || | |  | | | || |  || |     |  |   |
GACTGATCTCGGAAAGTAAATCGCAGC--CATGGCGGAAAAAGCTGTCACTATCAGGACCAGAAACTTCATGACCAACAGGCTTCTCGCCAGAAAGCAATTCgtgagttcccatctctatgttccattttgcaatctcacagtgttacgtcttcgctgtatcgaatgataaaaactatagtttag--gtagaaacaatcttata

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP07861 (Chlamydomonas reinhardtii), 5'ss of exon 1
CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacc-cgtg-----gcctcctttctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca
                     | |||  ||| | |||||| |||||||| | |||||||||||||||||||||||| |||||||     |   ||| ||||| ||     | ||     | || ||  || ||   | | |   |   | | | |     | ||  ||||| | | |   |                         
---------------------CGGCAAGATGTCGGACAAGACGTGCACTATCCGCACTCGCAAGTTCATGACCAACCGGCTGCTGCAGCGCCGGCAATTCgtgagtttggcatggagaaggctgctggctggccgcgcgctctggaggcctggacgc---tgac-tctcatcatattgcgcag-----------------------

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|162207611|gb|FC384064.1|FC384064
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162207612|gb|FC384065.1|FC384065
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162264253|gb|FC441355.1|FC441355
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162211993|gb|FC388455.1|FC388455
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162231344|gb|FC406767.1|FC406767
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162184761|gb|FC361063.1|FC361063
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162211994|gb|FC388456.1|FC388456
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162264252|gb|FC441354.1|FC441354
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTTTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|7147798|gb|AW509720.1|AW509720
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|67728029|gb|BJ978288.1|BJ978288
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCNTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162184760|gb|FC361062.1|FC361062
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
EST: gi|162252337|gb|FC427276.1|FC427276
EST:     TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTC                         ATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG
genomic: TGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG

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: 32 (upstream exon), 35 (downstream exon)
Score: 75

CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcaccc ... ttgcgtgcagATCATTGATGTGCTACACCCCGGTCGTGCTAATGTCTCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGCCCCAGCCAGCAGCAGCAGCATCATGGCTGACAAGGCGTGCACTGTGCGCACTCGCAAGTTCATGACCAACAGGCTGCTCGCCAGGAAGCAGTTCgtaagcacccgtggcctcctttctcgcttagggtttctggaacattggcttgtgtaacacctcattagagttttcgcttggttgtggttgtgacttctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT