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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGGGTCAACTGCCTCCACGGCCGTTTTGGTGGGCGATCGTTTACTTGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgcgacttctcatgagctttgtgctataccatgacaccactgtaagaaactgagaatttagtatgttgtacattttttacaatgagcagcacc...

Basic information

species Physcomitrella patens
transcript PP1S17_286V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 5
GATGCAGGGTCAACTGCCTCCACGGCCGTTTTGGTGGGCGATCGTTTACTTGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgcgacttctcatgagctttgtgctataccatg---acaccactgtaagaaactgagaatttagtatgttgtacattttttacaatgagcagcacc-
|||||||| |||||||| ||||| ||  |||| || || || || || |||||||| |||||||| ||||||||||| ||  | || |  || || || |||||  |||  |  | |    |  | ||        ||||   ||| |  | ||   | ||    |     | ||||||  ||| || |   ||      |   
GATGCAGGATCAACTGCTTCCACTGCTATTTTAGTTGGTGACCGCTTGCTTGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgtaagctttatacatatatgcatgcatgcatgcatacatctatctatttatctttagac---atgtgttgttaattattaattgtgt-tgttattg

upper sequence: PP1S17_286V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 5'ss of exon 4
GATGCAGGGTCAACTGCCTCCACGGCCGTTTTGGTGGGCGATCGTTTACTTGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgcgacttctcatgagctttgtgctataccatgacaccactgtaagaaactgagaatttagtatgttgtacattttttacaatgagcagcacc
||||| || |||||||| ||||| ||  || | || || ||||||||||||||||| |||||||||||||||||||| ||  | |||  ||| || || |||| |  |        |  |||  |  ||  |    | ||  | |  | | | |   |  ||| | | |   | || |  || |                
GATGCTGGTTCAACTGCTTCCACAGCTATTCTCGTTGGTGATCGTTTACTTGTTGCTAATGTTGGTGATTCCAGAGCTGTTATATGTCGTGGCGGAAATGgtacttttattgacatttttga-ttaagtcatgactcttggtatctat-tgaaatcttctgaaatgaattcat-gtgctcttgtag--------------
















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|162184832|gb|FC361134.1|FC361134
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|162157033|gb|FC333395.1|FC333395
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|208378728|gb|DC914702.1|DC914702
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|162243725|gb|FC421846.1|FC421846
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|100447095|gb|CJ971394.1|CJ971394
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|100447779|gb|CJ972078.1|CJ972078
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAAC
EST: gi|100401328|gb|BY990947.1|BY990947
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTTTNACTTTTCACTGACCACAAGCCCAATCGACATGATGAACGGGGAA
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGG-AA
EST: gi|100447201|gb|CJ971500.1|CJ971500
EST:     TGTTGCCNATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAG                         CCCTNCCACTTTCC-CTGAC-ACAN-CCCAATCGAC
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGAC
EST: gi|208384897|gb|DC907510.1|DC907510
EST:     TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGANGGAAAG                         CCCTTCC-CTTTCCACTGACCACAANCCNA-TCGACATGATGAACGG
genomic: TGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGG

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: 35 (upstream exon), 34 (downstream exon)
Score: 19

GATGCAGGGTCAACTGCCTCCACGGCCGTTTTGGTGGGCGATCGTTTACTTGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgc ... ttggcttcagCCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAGGGTCAACTGCCTCCACGGCCGTTTTGGTGGGCGATCGTTTACTTGTTGCCAATGTTGGTGATTCCAGAGCGGTGCTTTGTACTGGAGGGAAAGgtaatcgtgcgacttctcatgagctttgtgctataccatgacaccactgtaagaaactgagaatttagtatgttgtacattttttacaatgagcagcacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG