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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtgctttgagaagtcgacacctacgtgacattgcagaactttcggatacgtgtggagcgttgttgagttttcatctgattgatccgttgttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT

Basic information

species Physcomitrella patens
transcript PP1S27_81V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S27_81V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G112149_T01 (Zea mays), 3'ss of exon 4
gtaagtgtgctttgagaagtcgacacctacgtgacattgcagaactttcggatacgtgtggagcgttgttgagttttcatctgattgatccgttgttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT
                  ||   || | ||   |    ||  |    |    | |      | | ||||| | |  | || ||||      ||| |    |||||||| ||  |  | || ||||||| ||||||||| |||||||||||||| || ||||| |  ||||| |  ||||| || |||    | |  |  || || 
------------------gtaagcatccacacaaagcagcgaacaactttttttcagcataatctttgttaattgataatgtgatg----tgttatgaaatacagGGAGGTTGTTGCTGAGCTGAAGGCAGCTGGTGCTTCATGGATTCAGCTTGATGAGCCTACCCTTGTTAAAGACCTTGATGCTCACGAATTGGCCGCATTC

upper sequence: PP1S27_81V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 4
gtaagtgtgctttgagaagtcgacacctacgtgacattgcagaactttcggatacgtgtggagcgttgttgagttttcatctgattgatccgttgttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT
                  ||   || | ||   |    ||  |  |||     | |  ||   | | ||| | |  | || ||||  ||   || |    |  ||||| ||  |  | |||||||||| ||||||||| |||||||||||| | || ||||| |  ||||| |  ||||| || | |    | |  |  || || 
------------------gtaagcatccacacaaagcagccaacattttttcca-gcatgattc-tcgttaattgataatgtgat--att--ttatgaaatgaagGGAGGTTGTTTCTGAACTGAAGGCAGCTGGTGCTTCATGGATTCAGTTTGATGAGCCTACCCTTGTTAAAGACCTTGATGTTCACGAATTGGCAGCATTC
















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|100378044|gb|BY949652.1|BY949652
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
EST: gi|162271433|gb|FC447006.1|FC447006
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
EST: gi|18354666|gb|BJ186724.1|BJ186724
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
EST: gi|100405134|gb|BY955379.1|BY955379
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
EST: gi|100446848|gb|CJ971147.1|CJ971147
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
EST: gi|67569431|gb|BJ942255.1|BJ942255
EST:     AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAA                         GGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA
genomic: AAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGA

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: 30 (upstream exon), 35 (downstream exon)
Score: 9

TTGGACCAGTGACCTATTTGCTTTTGTCTAAGGGTGACAAGTCTGCACCCAAGGGATTCGACACTCTTTCTCTTCTGGACGCCATCCTCCCTGTTTACAAgtaagtgtgc ... ttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacgtgtggagcgttgttgagttttcatctgattgatccgttgttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT
                                gattgat  putative branch site (score: 9)
                       ttttcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtgctttgagaagtcgacacctacgtgacattgcagaactttcggatacgtgtggagcgttgttgagttttcatctgattgatccgttgttcgttacagGGAAGTAATCACGGAACTGAAGGAAGCTGGTGCCTCATGGATTCAGCTGGACGAGCCCAAGCTTGTCATGGACCTAGAAGCTGCTCAGTACGAGGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT