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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgcctcgtgaagacttgtttatcagctagatcaaggatattcgaatttttcctgtactggcagaaggttctgcgagatcattgaatatgtcttggattctaatttgagcggtcaagtctgcatgattcgtgttatctcataatggctgcggtggcggttgggattgtggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S269_30V6.2 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 13
gtatgatgcctcgtgaagacttgtttatcagctagatcaaggatattcgaatttttcctgtactggcagaaggttctgcgagatcattgaatat-gtcttggattctaatttgagcggtcaagtctgcatgattcgtgttatctcataatggctgcggtggcggttgggat-tgtggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG
                                                                             | |||||     || || ||     || ||||| |   |  |||    ||  |  ||| |         || ||       |    ||||  ||   ||||   |||||  |  | || ||||| ||| |||||||||||||||||||| | || || |||||||||| |
-----------------------------------------------------------------------------gtgagatttgcaaacatagtgcataatactaatcta--ccatcatccttgttt--ttccttcctggaattagtgctcatattttgagttgccatgcatgga---cagGGAAGGATGATACTTGCTCATTTATGTGATGAACCCAAAGGTCTCAAAACTGGAATGTGCATG

upper sequence: PP1S269_30V6.2 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G466281_T01 (Zea mays), 3'ss of exon 13
gtatgatgcctcgtgaagacttgtttatcagctagatcaaggatattcgaatttttcctgtactggcagaaggttctgcgagatcattgaatatgtcttggattctaatttgagcggtcaagtctgcatgattcgtgttatctcataatggctgcggtggcggttgggattgtggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG
                                                                              |  | | |||  || | |||    ||  |  |       |  |||     |  | |  || |    || |    | |  |     |    ||  ||     |||||  || | ||||| || ||  | |||||||||||||| |||||||| ||||| ||||||| |
------------------------------------------------------------------------------catgcttattttatttttctc---ttacagatgccctctttcagttactgtagtgca-gtaaaaatatgaacattactttacatctgcttatattgctccacagGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATG
















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|37840929|gb|BJ598937.1|BJ598937
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCNTTCGCTTACNTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|162255598|gb|FC431596.1|FC431596
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|162279090|gb|FC455429.1|FC455429
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208386299|gb|DC953012.1|DC953012
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208348107|gb|DC916917.1|DC916917
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|67696733|gb|BJ956966.1|BJ956966
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208376570|gb|DC922601.1|DC922601
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|162183659|gb|FC359900.1|FC359900
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208381414|gb|DC927850.1|DC927850
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208344725|gb|DC905174.1|DC905174
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAGCCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|162189304|gb|FC366774.1|FC366774
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208394434|gb|DC928486.1|DC928486
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208354437|gb|DC926614.1|DC926614
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208397506|gb|DC916390.1|DC916390
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|18334107|gb|BJ166123.1|BJ166123
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208347298|gb|DC925322.1|DC925322
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208356794|gb|DC926805.1|DC926805
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208363842|gb|DC943299.1|DC943299
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208395040|gb|DC924175.1|DC924175
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208380224|gb|DC919060.1|DC919060
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAGCCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208355907|gb|DC926668.1|DC926668
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|100395052|gb|BY953582.1|BY953582
EST:     A-CCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
EST: gi|208354673|gb|DC918699.1|DC918699
EST:     AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG                         GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA
genomic: AACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACA

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: 23 (upstream exon), 32 (downstream exon)
Score: 9

GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTGgtatgatgcc ... tggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattcgtgttatctcataatggctgcggtggcggttgggattgtggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG
               tcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgcctcgtgaagacttgtttatcagctagatcaaggatattcgaatttttcctgtactggcagaaggttctgcgagatcattgaatatgtcttggattctaatttgagcggtcaagtctgcatgattcgtgttatctcataatggctgcggtggcggttgggattgtggattgcagGGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA