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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAAGGAGAGGACTGTTAAGGAACAAATGGTACGCGATTCAACTGAGGTGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtctcctgttagtgttccaccggaactttcggatgttactgaatgaatgttgctaatggtattttgaagttttcacggctggagaacttgcaag...

Basic information

species Physcomitrella patens
transcript PP1S347_31V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S347_31V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G163473_T01 (Zea mays), 5'ss of exon 4
TGTGAAGGAGAGGACTGTTAAGGAACAAATGGTACGCGATTCAACTGAGGTGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtctcctgttagtgttccaccggaactttcggatgttactgaa--tgaatgttgctaatggtattttgaa-gttttcacggctggagaacttgcaag
| ||||||| ||||   | ||||| || ||||     ||  ||||||| ||| |||| ||||| || |  |||||||||||||||||||| || || ||||||||||   |     |   |     |       |      |||   ||  ||   |    |  | |     |||  ||     |   | |     |||    
TTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaactgtgaaacttcatttctctttcattctgcattagaaaacctgggcgcgctttgtcgcgccatgattgtgccagccagtagcagttttgt---

upper sequence: PP1S347_31V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 5
TGTGAAGGAGAGGACTGTTAAGGAACAAATGGTACGCGATTCAACTGAGGTGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtctcct-gttagtgttccaccggaactttcggatgttactgaatgaatgtt-gctaatggtattttgaagttttcacggctgga-gaacttgcaag
| ||||||| ||||   | ||||| || ||||     ||  ||||||| ||| |||| ||||| || |  |||||||||||||||||||| || || ||||||||||   | | |||  | || ||      | ||||    |||     ||  |    |     |     |||| |  |   || | ||  |  | ||    
TTTGAAGGAAAGGAGGCTCAAGGACCAGATGGAGAAAGACCCAACTGAAGTGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaactttgtttatctttcattatg-cattcgagccttagaccctgttttcaagtcgtcgactagttgacgactagtcgtccggtcggtcctggg--
















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|208372253|gb|DC948056.1|DC948056
EST:     ACCGCATGCTT-CCCGCAAC-AGCTCCGAGAT                         GATAGGATGCTGAAGNTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: ACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|208391203|gb|DC942087.1|DC942087
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|67578563|gb|BJ950730.1|BJ950730
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|208347748|gb|DC912923.1|DC912923
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|208394250|gb|DC933918.1|DC933918
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|208369000|gb|DC955085.1|DC955085
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACCAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|208355032|gb|DC926697.1|DC926697
EST:     AAAGCCGTCCACCGCATGCTTCCCCGCAACCAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: AAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|162215635|gb|FC391688.1|FC391688
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTCCGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|22492604|gb|BU052527.1|BU052527
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
EST: gi|22491678|gb|BU051601.1|BU051601
EST:     TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGAT                         GATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC
genomic: TGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCC

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: 19 (upstream exon), 31 (downstream exon)
Score: 3

TGTGAAGGAGAGGACTGTTAAGGAACAAATGGTACGCGATTCAACTGAGGTGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtct ... ggtttcgcagGATAGGATGCTGAAGTTACGTATATTCCCTGAGGAAGAGCATCCGTTTCCCCCCGAGCAGATGGATAAATTTGAGATGCCTCCACGCAAAGTGCGTGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAAGGAGAGGACTGTTAAGGAACAAATGGTACGCGATTCAACTGAGGTGCTTCGTAAAGCCGTCCACCGCATGCTTCCCCGCAACAAGCTCCGAGATgtaagtgtctcctgttagtgttccaccggaactttcggatgttactgaatgaatgttgctaatggtattttgaagttttcacggctggagaacttgcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT