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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagtctttatcttttaactctggtttttgtcatggggtgtttgtttggcactgtgcaatgttagtcgtggttaatccgtttgtaaatccttagattcccttaatttttcatctctctcctgaaaagtgaagttctgaatctgtattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAGGGCGATCCATTTACCTTCACAATTAAGCGTGGAGTGGGAACGGATACGT

Basic information

species Physcomitrella patens
transcript PP1S205_25V6.1
intron # 1
splice site 3'
intron type U2

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|162153879|gb|FC330010.1|FC330010
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|100407600|gb|BY991774.1|BY991774
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162178857|gb|FC354789.1|FC354789
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162169105|gb|FC345995.1|FC345995
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162156500|gb|FC332108.1|FC332108
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|208350245|gb|DC901615.1|DC901615
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTANGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|208360056|gb|DC939332.1|DC939332
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|208374258|gb|DC941127.1|DC941127
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162278586|gb|FC454048.1|FC454048
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|100359011|gb|BY946801.1|BY946801
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGGTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAA
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162187679|gb|FC364630.1|FC364630
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|208367109|gb|DC935937.1|DC935937
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|208374609|gb|DC931962.1|DC931962
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTANGANTGGAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAG
EST: gi|162179457|gb|FC355457.1|FC355457
EST:     CTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: CTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162159393|gb|FC334661.1|FC334661
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
EST: gi|162181032|gb|FC358686.1|FC358686
EST:     ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAG                         GGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG
genomic: ACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAG

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: 33 (upstream exon), 34 (downstream exon)
Score: 10

GCACGGGGATCACGCCTCGCACAAGAAGGTGATTGATCTCGTGCGGGAGTACAACAAGGAAGCGAACGCGAATGTCATTGCCCTCATGCTTGATACCAAGgtttgtagtc ... tattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAGGGCGATCCATTTACCTTCACAATTAAGCGTGGAGTGGGAACGGATACGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaatttttcatctctctcctgaaaagtgaagttctgaatctgtattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAGGGCGATCCATTTACCTTCACAATTAAGCGTGGAGTGGGAACGGATACGT
 ccttaat  putative branch site (score: 10)
     atttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagtctttatcttttaactctggtttttgtcatggggtgtttgtttggcactgtgcaatgttagtcgtggttaatccgtttgtaaatccttagattcccttaatttttcatctctctcctgaaaagtgaagttctgaatctgtattctacagGGCCCAGAGGTTAGGAGTGGAGACTTGCCACAACCTATTATGCTAAAGAAGGGCGATCCATTTACCTTCACAATTAAGCGTGGAGTGGGAACGGATACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG