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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTCCCGAATCCTGCAATATGTTTACTTTTCTGTTTGATGACATTGGTATTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctggatataataattggttccagctgcgtcggtcataacagagtttttgcgcgtgcagatgctgagtttacccttgaagatttaatactgttcttggtgcaaccgtgctcacaatgatgtttcaacgtgcag

Basic information

species Physcomitrella patens
transcript PP1S422_8V6.1
intron # 4
splice site 5'
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|162174038|gb|FC350553.1|FC350553
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGA
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGA
EST: gi|100377031|gb|BY949584.1|BY949584
EST:     CTGC-GACTNAC-GTCACATGGAAGGGTTTCGGTGTACATACTTTTCAAG                         T-GATTAACAAGGCTGGNAAAGAA-CCTATGTCAGGTTTCACTGGA-GCC
genomic: -TGCCGACT-ACCGTCACATGGAAGG-TTTCGGTGTACATACTTT-CAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCC
EST: gi|208353793|gb|DC906481.1|DC906481
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162225471|gb|FC401223.1|FC401223
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162153220|gb|FC329002.1|FC329002
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162240135|gb|FC418262.1|FC418262
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162212922|gb|FC388930.1|FC388930
EST:     TTCCTGCCGACTACCGTCACATGGAAAGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTT-CACTGGAAGC-T
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162179286|gb|FC356235.1|FC356235
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|100444734|gb|BY982563.1|BY982563
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162200569|gb|FC376764.1|FC376764
EST:     TCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTNCA-G                         TTGATTAACAAGGCTGGAAA
genomic: TCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTT-CAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAA
EST: gi|100393831|gb|BY953524.1|BY953524
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162267693|gb|FC443475.1|FC443475
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162170490|gb|FC347649.1|FC347649
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGG
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGG
EST: gi|162221788|gb|FC398355.1|FC398355
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162175799|gb|FC352101.1|FC352101
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|67507796|gb|BJ940673.1|BJ940673
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162162217|gb|FC337999.1|FC337999
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162185084|gb|FC362218.1|FC362218
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162185869|gb|FC360969.1|FC360969
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
EST: gi|162263644|gb|FC438880.1|FC438880
EST:     TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAG                         TTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT
genomic: TTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCT

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), 35 (downstream exon)
Score: 70

CGTTCCCGAATCCTGCAATATGTTTACTTTTCTGTTTGATGACATTGGTATTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctgg ... caacgtgcagTTGATTAACAAGGCTGGAAAAGAAACCTATGTCAAGTTTCACTGGAAGCCTACATGCGGTGTGAAGAATCTGTTGGACGATGAGGCTGTGCTAGTCGGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTCCCGAATCCTGCAATATGTTTACTTTTCTGTTTGATGACATTGGTATTCCTGCCGACTACCGTCACATGGAAGGTTTCGGTGTACATACTTTCAAGgtacgtctggatataataattggttccagctgcgtcggtcataacagagtttttgcgcgtgcagatgctgagtttacccttgaagatttaatactgttcttggtgcaaccgtgctcacaatgatgtttcaacgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG