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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaccaatatcaaactttgtttcccttttgtatgttttgttctgcacctttgcattcaggtgccacagaggctctgatcaagtttggtgttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA

Basic information

species Physcomitrella patens
transcript PP1S99_42V6.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_42V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
--gtacaccaatatcaaactttgtttcccttttgtatgttttgttc-tgcacctttgcattcaggtgccacagaggct--ctgatcaagtttggtgttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA
   |||  |  | | | | | || |     ||  |||||  |  |  | |   |      |||  |          ||  ||  | || |||    |  || |||| ||||||||||| || ||||||||||||||||||||  |    |||   |  ||  | || || |        |   | |||||| ||||  | |||  
ctatacttctttcttagattgtggtgg---ttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaattt--catccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG
















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|100440899|gb|BY962387.1|BY962387
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|100379974|gb|BY968783.1|BY968783
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCAGGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|162195534|gb|FC371835.1|FC371835
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|208386797|gb|DC937189.1|DC937189
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|162257183|gb|FC433059.1|FC433059
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|100437064|gb|BY961333.1|BY961333
EST:     TCTGCTAGCGAGCTGACACCTAACACTGAATATGGGATCGGGGTCAAATG                         GGGGTTTTAATCAACCTATTATG
genomic: TCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAA-TGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATG
EST: gi|162226251|gb|FC402959.1|FC402959
EST:     ATGGAATCGGGTTCAATGG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCG
genomic: ATGGAATCGGGTTCAAT-Ggtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCG
EST: gi|100427559|gb|BY977558.1|BY977558
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|100386075|gb|BY970014.1|BY970014
EST:     GTCTGCTTGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|162159901|gb|FC336154.1|FC336154
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|162227790|gb|FC402705.1|FC402705
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|67508225|gb|BJ941096.1|BJ941096
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
EST: gi|100440507|gb|BY962234.1|BY962234
EST:     GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGGTCAATG                         GGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA
genomic: GTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGA

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), 35 (downstream exon)
Score: 21

GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATGgtacaccaat ... gttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacctttgcattcaggtgccacagaggctctgatcaagtttggtgttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA
                                            tgttgat  putative branch site (score: 21)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaccaatatcaaactttgtttcccttttgtatgttttgttctgcacctttgcattcaggtgccacagaggctctgatcaagtttggtgttgatgcagGGGGTTTTAATCAACCTATTATGTGTGGTGGTGAGCCGCGTATCATGGCGAAGAAGGAACGTGGAAGTCTATGCGAGACCATATATGCCATCAAAATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG