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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagaaagtagctctcgtgtttttattccacagcttaattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA

Basic information

species Physcomitrella patens
transcript PP1S340_7V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
-cgagaa--agtagctctcgtgtttttattc-cacagcttaattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
 | |  |  || |  |   || |   ||||       | || |   |        ||||     ||   || ||  ||| |   ||  | ||    |  |  ||||  ||||  | || || || ||||||||||| ||||||||||||||| ||||||| ||||| ||||||| |||||| ||||| ||  ||||||| ||||
gctattaccagaaattgctgtttccctattaatgtgacctattgttttggaacaattgcgtattgtaaccatatggtttctgcttt--tctcaa--ctgtttagATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 2
cgagaaagtagctctcgtgttttt----attccacagcttaattcct---gtttttcgttgcaaccggttgtcagat--attttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
       ||   | ||| ||  ||    ||  || |||  ||||| |     || |  ||      | ||||  |    | |||  |||||  || |       | |||||||||||  | || || || ||||| ||||||||||||||||| ||  | ||| |||| || ||||||| |||||| || || || |||||||||||||
-------gtc-ttttcgagtccttgagaatgtcagagcagaattcttcgtagttctaattctgcaagattgtgggggcaaatttacaagttc-ttacttcctatttcagATATTGGAAATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
cgagaaagtagctctcgtgtttttattccacagc-ttaattcctgtttttcgttgcaaccggttg--tcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
    | | ||  | | || ||| |    ||  |  |   | | |  |||   |||   | || |   ||| |||     |   ||  | ||       |  |||| |||||  | || || || ||||||||||| ||||||||||||||  ||||||| ||||| ||||||| |||||| ||||| ||  ||||||| ||||
ttccatatta--tttggtctttgtcaggcagggtgtctgtacattatttattttgtttctgggttactcatatacagcctgcctttttctcaactattt-tagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 2
cgagaaagtagc--tctcgtgtttttattccacagcttaattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
  |||   |     |     |||||||      |    |  | |        | ||  ||    ||      |||  |||  |  || ||       |  |||| |||||  | || || || ||||| |||||||| |||||||||||  | ||| ||||||| ||||||| |||||| ||||| ||  ||||||||||||
taagattttcatatttcaaagtttttaagatgtaaggaagctgcatacccaaggtg-gacgatatgggctccattacttatatacatctcaactgttt-tagATTTTGGAAATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 2
-------------------------cgagaaagtagctctcgtgttttt---attccacagcttaattcctgttt--ttcgttgcaaccggttgtca---gatattttttaa--gtt----gatttcggtgc------------cctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
                            | | || |   | | | ||||     |    |   | | || |||    |   | | ||   |||||     ||| |||| | |  |||    ||||  |  |             | |  ||||||||||  | || |||||||| ||||||||||| |||||||| ||| ||||| | ||||| |||||||  ||||||||||| ||  | ||||| || |
gtagctacattgtttgtttctctgttttggatgttgtatttgggatttttgggctttgaattctgaatcttgtggaatggatggaaaaaagttgtttcttgattttttctcattgttcttggattatgacgtgataactttttgcatttagATATTGGAAATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
cgagaaagtagctctcgtgtttttat---tccacagct-taattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
  |   | |  |        ||| |     |   ||   | ||||   | |||  |     ||   |||   | ||| |   |  |||| |   ||   | |||||||||||  | ||||||||||||||||| ||||| |||||| | ||  ||||| | ||||| ||||||| |||||| ||||| ||  | |||||||| |
-aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattct--gacatgatatttttgtttt-cagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 2
-------------------------cgagaaagtagctctcgtgttttta---ttccacagcttaat-tcctgtttttcgttgcaaccggttgtcagatattttttaag---------ttgatttcggtgc------------cctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
                            | |  | |   | |  |||||    ||  |   || ||| | |||   |   | | ||   |||||    |  |||||||          ||||||  |  |             | |  ||||||||||  | || || ||||| ||||||||||| |||||||| ||| ||||| | ||||| |||||||  ||||||||||| ||  | ||||| || |
gtacctatattgtttgtttctctgttttggatattgtattgggatttttggacttttaattctgaatcttctggaatggatggaaaaaagttgtttcttgatttttaaacatttttcattgattatgacgtgataattttttgcatttagATATTGGAAATGAACCCGGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
-cgagaaagtagctctcgtgtttttattccacagcttaattcctgtttttcgttgcaaccggttgtcagatattttttaagttgat-ttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
      || ||| | || | | ||  ||       ||   | | |  | |            |||     ||  | ||  |||    |    |||  |  |||| |||||  | |||||||||||||| ||||| || |||||||| ||| ||||| | ||||| ||| ||| |||||| ||||| || ||||| || || |
gtattcaactagttttcttatcttatttttggtattttcctacagagtcttacctatttgatttgaattctaactgttgtgttaccatatcatgctat-tagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 3
-cgagaaagtagctctcgtgtttttattccacagcttaatt-cctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
        |  ||| | |  || |||   | |||| || ||   | | |||  ||        |||  | ||||||    |     | | ||||   |  |||| |||||  | || |||||||||||||||||||| ||||| ||||| |||||| | ||||| ||||| | |||||| |||||||| ||||| || || |
ctcctgttgctgctattgctttattaacacccagcgtatttgtttatattttattttttatttttggtaaatatttaactacagtttgttggtgtttt--agATTTTGGAAATGAACCCAGAAGATGAAGCTGAAGAAGATGGCGCTAACGTTGATCTTGACTCCCAAAGAAAAGGAAAATGTGTCGTGTTGAAAACCTCTA

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|100446734|gb|CJ971033.1|CJ971033
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208366108|gb|DC935869.1|DC935869
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208373535|gb|DC941104.1|DC941104
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCGATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
EST: gi|208382087|gb|DC914776.1|DC914776
EST:     AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAG                         ATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT
genomic: AGATCAAACTCAATAAACAGCTGCCTTACCTAGTTGGAAACATTGTGGAGgttggtgttg ... tgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA
                                 agttgat  putative branch site (score: 5)
                     agatattttttaagtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgagaaagtagctctcgtgtttttattccacagcttaattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA