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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaagtgtttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG

Basic information

species Physcomitrella patens
transcript PP1S348_15V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0014g01420.t01 (Vitis vinifera), 3'ss of exon 2
tggaagtgtttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG
 | |||   | | |||   |||  |   |||| |||  | || |||  |||  |||  ||  ||  |    ||||       || | |      | ||||||| || ||||| ||||||||  ||||||||||||||||||| |||||||| ||||| || || || || ||| | ||||| ||||||
-gtaaggaatatgtttgagtttggtgcattttatttcatttgagtgctttgatttt--tgtagtaatttcagggtt------tggttg------tttcagGAAAGGGGATTATTATCGGTACCTGGCGGAGTTCAAGACCGGCAATGAGAGGAAAGAGGCGGCTGATCAGTCTCTTAAGGCATACCAG
















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|37827533|gb|BJ585545.1|BJ585545
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTNTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208390694|gb|DC937850.1|DC937850
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162269401|gb|FC445269.1|FC445269
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67725735|gb|BJ975994.1|BJ975994
EST:     GAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: GAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208385562|gb|DC937107.1|DC937107
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67727562|gb|BJ977821.1|BJ977821
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGCGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162207491|gb|FC383736.1|FC383736
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67726117|gb|BJ976376.1|BJ976376
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67726885|gb|BJ977144.1|BJ977144
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162270401|gb|FC447101.1|FC447101
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67718418|gb|BJ968677.1|BJ968677
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208370697|gb|DC936157.1|DC936157
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67719261|gb|BJ969520.1|BJ969520
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGCGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208345060|gb|DC925641.1|DC925641
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208362548|gb|DC943747.1|DC943747
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208358628|gb|DC949963.1|DC949963
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18341253|gb|BJ173287.1|BJ173287
EST:     TCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162249893|gb|FC425694.1|FC425694
EST:     AACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: AACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|67726399|gb|BJ976658.1|BJ976658
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|100373556|gb|BY948980.1|BY948980
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|37852754|gb|BJ610762.1|BJ610762
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208387877|gb|DC929221.1|DC929221
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162269402|gb|FC445270.1|FC445270
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|37830224|gb|BJ588236.1|BJ588236
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208365445|gb|DC950912.1|DC950912
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|18338400|gb|BJ170424.1|BJ170424
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGNCCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|37846290|gb|BJ604298.1|BJ604298
EST:     CCGTCGTCGAGCACGGGCGAGTCAACGGTGTTNTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: CCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|162207492|gb|FC383737.1|FC383737
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
EST: gi|208354137|gb|DC957385.1|DC957385
EST:     TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGAT                         GAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG
genomic: TTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAG

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: 17

AAGAGCTTTCGAAGATTTGTCAGGACATACTGACGATCATCGACGAGCACTTGATTCCGTCGTCGAGCACGGGCGAGTCAACGGTGTTCTACTTCAAGATgtacgtgatg ... gggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaagtgtttttttttttttttttttttttttttttgtgtgtgtgtgttgtgtttgctgaggtggtgatggggtggatatgtgatgggcgggatatcagGAAGGGTGATTACTATCGGTATTTGGCGGAGTTCAAGACCGGGAATGAGAGAAAAGAAGCCGCCGACCAATCTTTGAAGGCGTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG