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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatggaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG

Basic information

species Physcomitrella patens
transcript PP1S98_222V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 4
actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatg---gaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
 |||| |  ||   |  |   ||         |     |||   |||  | | ||||  |   | | |    | | | |    | |  |  |  |   | |||||||| ||||||||||| ||||| ||||||||||| |||||| | || | |
-ctatttgctagcatt-tgcaatcttcatcagtttgttttccccttttttta-atatcatcttagttccaaaagtaaagcttaactcctgcgctttcctgcagGCAGGGTATGTAGGAGAAGATGTAGAATCTATACTATACAAGTTACTGGCG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g19150.1 (Oryza sativa), 3'ss of exon 4
---actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatggaatgttttgactctgtt-cagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
     | | | | |   || |||     ||     ||| |    ||| | |    | |  |   ||| | |  || ||| |  |   | ||    |  ||  |||| |||||||| || ||||||||||||||||| || || |||||||||| |
gcttttgtttgagagcgtcgtatagcagcttgatttaataa---gtgctcatgctggtgct-caggagttcaccttttctttaaccatgtttttccaattgtagGCTGGATATGTTGGCGAGGATGTTGAATCTATCCTGTATAAGCTCCTAGCG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 4
actatctcataattt-catatgattactgatcctaa-aacttcgtgtttactaagatattgtgggaatccttctattcatgg--aatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
    | |  || |   |||||| |  ||||  ||   |  ||  | |   | | | |||  |     |      | | | |   ||  |||  |||   | |||||||| ||||||||||||||||| ||||||||| | |||||| | ||   |
----tttgctattgcacatatggtctctgactctgttagatttctttccccgatgctatcctcttggtttcagcactaaggattaaattttccacttattgcagGCAGGTTATGTAGGAGAGGATGTAGAATCTATATTATACAAGTTACTCACG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G050186_T05 (Zea mays), 3'ss of exon 4
actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatgg--aatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
  | | |    ||| || || ||      |  || |      |    | |   ||    | ||  |  |   | | | ||  ||  |||  |||   | |||||||| ||||||||||| ||||| ||||||||| | |||||| | ||   |
tgtgttttgctattgcacat-atggtctctattagattcctttccccaattctatccacttggt-ttttagcactaagggttaaattttccacttattgcagGCAGGGTATGTAGGAGAAGATGTAGAATCTATATTATACAAGTTACTCACG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G41400.1 (Glycine max), 3'ss of exon 4
---actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatggaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
   | |||       ||||| |    |  | ||| |||   || || | |    |     |||     ||       | |    | || |   ||     |||||||| ||||| ||||||||||| ||||| ||| | |||||||||||  ||
gtgattataatcatctttcaaaaatgttttcatcttaat-ttttgt-tctgtggaagccatgtttatgtcacatgtctaacctca-gtgtcaccttcaaacagGCAGGTTATGTTGGAGAGGATGTAGAATCCATATTATACAAGCTCCTCATG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G13450.1 (Glycine max), 3'ss of exon 4
---actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaag-atattgtgggaatccttctattcatggaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
       | |   |  |||| |    |  | ||| |||   ||  | | |   ||  || ||   |  |    ||||  |   |    | |   || ||  |||||||| ||||| ||||||||||| ||||| ||| | |||||||||||  ||
tatgtcttattccatcttcaaaaatattttcatcttaatttttgctctgtggaaaccatgtttatgtcacgtgtctaacctcag----tgtcacctttgaacagGCAGGTTATGTTGGAGAGGATGTGGAATCCATATTATACAAGCTCCTCATG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv16s0098g01860.t01 (Vitis vinifera), 3'ss of exon 4
actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttct-attcatgg-aatgttttgactctgtt--cagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
      |  |  |||  | | || | | |    | |  |  |     | | |  | ||  |    || || | | |  ||| ||||     |   | ||  |||||||||||||| || || ||||| ||||||||| | |||||||||||  ||
------tggttgttt--ttttataagttacaagagagttatgaagaaatttaagttttaagtttttctttttcacttgtgggaatgacaaaatgttatttgcaggcagGATATGTTGGGGAAGATGTGGAATCTATATTATACAAGCTCCTCATG

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|162179889|gb|FC355960.1|FC355960
EST:     CGTCATTGCTGACGCTACGAGTCTCACGCAG                         GCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
genomic: CGTCATTGCTGACGCTACGAGTCTCACGCAGgtaactgatc ... ctctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
EST: gi|162174224|gb|FC350607.1|FC350607
EST:     ATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACGNCAG                         -CAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAG
genomic: ATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACG-CAGgtaactgatc ... ctctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAG
EST: gi|162247501|gb|FC425067.1|FC425067
EST:     GATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACGCAG                         GCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
genomic: GATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACGCAGgtaactgatc ... ctctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
EST: gi|162178158|gb|FC354876.1|FC354876
EST:     GATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACAAGTCTCACGCAG                         GCAGGGA-ATGTAAGAGAGGATGGTT-AATCTATACTTTACAAG
genomic: GATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACGCAGgtaactgatc ... ctctgttcagGCAGG-ATATGTAGGAGAGGATG-TTGAATCTATACTTTACAAG

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: 2

GTAAAACATTGCTTGCCAAAACCTTGGCTAGATTTGTAAATGTACCTTTCGTCATTGCTGACGCTACGAGTCTCACGCAGgtaactgatc ... ctctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactaagatattgtgggaatccttctattcatggaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG
                                       ttttgac  putative branch site (score: 2)
                                             ctctgttc  CT-rich tract
     aagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatctcataatttcatatgattactgatcctaaaacttcgtgtttactaagatattgtgggaatccttctattcatggaatgttttgactctgttcagGCAGGATATGTAGGAGAGGATGTTGAATCTATACTTTACAAGCTCCTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT