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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgtcaccatcttgcgtgcatttcccttcatcgtctaataaagtaacacgattattagaaggtgcaagagcgcctgcagtaatgtgtgcagctt...

Basic information

species Physcomitrella patens
transcript PP1S214_34V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 12
GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATT------CCACTgtaagctcgtcaccatcttgcgtgcatttcccttcatcgtctaat---aaagtaacacgattattagaaggtgcaagagcgcctgcagt--aatgtgtgcagctt---------------
 |||||||||||||| |||||||| ||||||||| |||||||  | |||||||| || ||          | | ||   || |      ||  |     |       || | | | ||   | | || |    | || ||    |  ||  |  | |  | |  ||||| | ||  ||               
AGTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCGgttagtatacattctttgttggctctcacaagtaaagaaacagcttatgattccacattatcctcctcatcagggaatctaaacgtccatatattcaaatgttttcatttttgttggttgtgaaag

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 12
GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATT------CCACTgtaagctcgtcaccatcttgcgtgcatttcccttcatcgtctaat---aaagtaacacgattattagaaggtgcaagagcgcctgcagt--aatgtgtgcagctt---------------
  ||||||||||||| |||||||| ||||||||| |||||||  | |||||||| || ||          | | ||   || |      ||  |     |       || | | | ||   | | || |    | || ||    |  ||  |  | |  | |  ||||| | ||  ||               
--TTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCGgttagtatacattctttgttggctctcacaagtaaagaaacagcttatgattccacattatcctcctcatcagggaatctaaacgtccatatattcaaatgttttcatttttgttggttgtgaaag

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 12
GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgtcaccatcttgcgtgcatttcccttcatcgtctaataaagtaacacgattattagaaggtgcaagagcgcctgcagtaatgtgtgcagctt
 ||||||||||||||||| ||||| |||||| | ||||||||| | || || || || ||     | ||| | || | || | | |      | |    |  ||||   | ||| | ||   | | | |   |  ||     ||     ||  ||| |||       
AGTTCCAAACATCAAGTTCAACGTTGCCAAACTTCTGCAATCCCTCATCCCCATAGTCGACCAATCAgtacgatcataacaaacata-----actcagttatatcgaaaactaatggaaattgttgaattttaa-tgtttttgccgtgtcaaaaatttgtag-----

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|37829837|gb|BJ587849.1|BJ587849
EST:     TTNACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCTT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|18338950|gb|BJ170976.1|BJ170976
EST:     TTAACGTCGCCAAAATNNTGCAATCCATGATTCCGATTGTTGATTCCNCT                         GTTGTGGAGCAAACAATTCTGGCCATGCTTGTTGGAACTTCAGGAAGACCC
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTC-GGCCATGCTTGTTGGAACTTCAGGAAGACCC
EST: gi|37821365|gb|BJ579431.1|BJ579431
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|208392785|gb|DC953682.1|DC953682
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|18335295|gb|BJ167313.1|BJ167313
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37821299|gb|BJ579365.1|BJ579365
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37821624|gb|BJ579690.1|BJ579690
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37828113|gb|BJ586125.1|BJ586125
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCNTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162153519|gb|FC330120.1|FC330120
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37843689|gb|BJ601697.1|BJ601697
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162181338|gb|FC357081.1|FC357081
EST:     ATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: ATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162170520|gb|FC347666.1|FC347666
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162179207|gb|FC355672.1|FC355672
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37829768|gb|BJ587780.1|BJ587780
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37830897|gb|BJ588909.1|BJ588909
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37845416|gb|BJ603424.1|BJ603424
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162254923|gb|FC431108.1|FC431108
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37841224|gb|BJ599232.1|BJ599232
EST:     TAACGTCGCCAAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TAACGTCGCC-AAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162258176|gb|FC433958.1|FC433958
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37844214|gb|BJ602222.1|BJ602222
EST:     TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT

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: 24 (upstream exon), 35 (downstream exon)
Score: 11

GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgt ... tcccttacagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCTGATGTGGATGTCCGATTTTTTGCGGGCCAGGCTCTGCAAGCATGTGACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACTgtaagctcgtcaccatcttgcgtgcatttcccttcatcgtctaataaagtaacacgattattagaaggtgcaagagcgcctgcagtaatgtgtgcagctt

- - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - TGCTGC