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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTATCCGCATTTTCTTGAACGATGGTCATCAAATTGCATGTGCACAGTCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatttatgattcctgttctgtatggctacatgattccaaaaatattttttttaactatatcaactaacaaattagtaatttaaggcttgtgtca...

Basic information

species Physcomitrella patens
transcript PP1S223_31V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S223_31V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 5'ss of exon 6
AGGCTATCCGCATTTTCTTGAACGATGGTCATCAAATTGCATGTGCACAGTCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt------tatgatt--cctgttctgtatggctacatgattccaaaaatattttttttaactatatcaactaacaaattagtaatttaaggcttgtgtca
|||| || || || ||  |  | ||||| |||||||||| |||||||||||| |  || || |||||||| |||||||| ||  | |  ||||| || |||| |    ||      | | |||  ||| || | |    || ||  |   ||     || | |||||| ||| |    |      |   || |||   |  | |    
AGGCAATTCGAATATTTCTTGAAGATGGACATCAAATTGGATGTGCACAGTCATATGCGAAAAACATGGGACTTTATGGACAAAGAGCAGGATGCCTTAGgtattcatttccctgttttaattgtcctttttttttcttctgcaacagctcattcccatctcttttaattatgtttgttt-----tggatattttcctgtctttt---

upper sequence: PP1S223_31V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G146677_T01 (Zea mays), 5'ss of exon 6
AGGCTATCCGCATTTTCTTGAACGATGGTCATCAAATTGCATGTGCACAGTCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatttatgattcctgttctgtatggctacatg-attccaaaaatattttttttaactatatcaactaacaaat-tagtaatttaaggcttgtgtca
|||| ||||| |||||| |  | ||||| || ||||||| |||||| ||||| | ||||||||||||||| |||||||| ||  | |  ||||| || |||| |    || |  | | |  | || | ||  |||||  | |      |  |  | |    ||   | || | |||  | |  |  |||  ||||||  |  
AGGCAATCCGAATTTTCCTTGAAGATGGACACCAAATTGGATGTGCTCAGTCATACGCAAAGAACATGGGACTTTATGGACAAAGAGCAGGATGCCTGAGgtattcagttgactagtgccttgctat-tgtatacatatagtgttgtcacctgctgtacttcttagtaaattgacatgtgtgatcttttggggcttgaatt-
















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|7286670|gb|AW599157.1|AW599157
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|37845929|gb|BJ603937.1|BJ603937
EST:     TTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|208369208|gb|DC955837.1|DC955837
EST:     TCTTTCGCAAAGNACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162256780|gb|FC432674.1|FC432674
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCG
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCG
EST: gi|19789721|gb|BQ041471.1|BQ041471
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162221031|gb|FC398283.1|FC398283
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162221032|gb|FC398284.1|FC398284
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162198688|gb|FC373469.1|FC373469
EST:     AAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: AAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162257989|gb|FC434083.1|FC434083
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|7286761|gb|AW599248.1|AW599248
EST:     TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: TCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|67725499|gb|BJ975758.1|BJ975758
EST:     GCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCNACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: GCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
EST: gi|162244629|gb|FC423452.1|FC423452
EST:     CTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAG                         TGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA
genomic: CTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCA

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: 31 (upstream exon), 10 (downstream exon)
Score: 2

AGGCTATCCGCATTTTCTTGAACGATGGTCATCAAATTGCATGTGCACAGTCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatt ... gaatggctagTGTTGTGTGCGACGATCCTCAACAAGCAGTTGCCGTGAAGAGTCAGTTGCAGCTGATTGCTCGCCCTATGTACTCCAACCCTCCCTTGCATGGTGCTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTATCCGCATTTTCTTGAACGATGGTCATCAAATTGCATGTGCACAGTCTTTCGCAAAGAACATGGGTCTTTATGGCCAGCGTGTTGGATGTCTCAGgtgtgttatttatgattcctgttctgtatggctacatgattccaaaaatattttttttaactatatcaactaacaaattagtaatttaaggcttgtgtca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaata