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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcatgaaaccatgatttaaatttgaacaatcttcaatcctcatggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG

Basic information

species Physcomitrella patens
transcript PP1S118_166V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S118_166V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 2
gtaatgtcatgaaaccatgatttaaatttgaacaatcttcaatcctcatggtg-tatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG
                 |||||    | ||||  ||    ||| ||  || |  |   ||| || |   |    |       ||  |  |  |    |    |||||  | || |||||||| ||  | | |||||||||||| ||||| ||||| |||||||| ||||| ||||| |  | |||||| ||||| ||  | ||||
-------------gtattgattatgttatgaa--atgcctaatgcttttgttaatgattaaattactgaacaaaaaa-----aacatcaatgc----ttttgcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG

upper sequence: PP1S118_166V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
gtaatgtcatgaaaccatgatttaaatttgaacaatcttcaatcctcatggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG
                ||||||  | | ||||    ||       |  ||   |   ||| || | | |  | | |   ||                    |||||  | || |||||||| ||  | | |||||||||||| ||||| ||||| |||||||| ||||| ||||| |  | |||||| ||||| ||  | ||||
--------------gtatgattatattatgaaatgcctcatgcttttgtga-atgagtaaattactaaacatcattgcttt------------------ttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG
















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|162184365|gb|FC359111.1|FC359111
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162180630|gb|FC356987.1|FC356987
EST:     CTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162156914|gb|FC333068.1|FC333068
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162191704|gb|FC367437.1|FC367437
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162155882|gb|FC332431.1|FC332431
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATG
EST: gi|162186129|gb|FC361333.1|FC361333
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162155563|gb|FC331007.1|FC331007
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162208920|gb|FC385264.1|FC385264
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162161676|gb|FC339091.1|FC339091
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162274886|gb|FC451121.1|FC451121
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162150526|gb|FC326174.1|FC326174
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATG
EST: gi|162164619|gb|FC341914.1|FC341914
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162176373|gb|FC353558.1|FC353558
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTNCA-GGT
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCT-CAAGGT
EST: gi|162156983|gb|FC333345.1|FC333345
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162159446|gb|FC336235.1|FC336235
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162150725|gb|FC327621.1|FC327621
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCCGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162184673|gb|FC361911.1|FC361911
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162167471|gb|FC344188.1|FC344188
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTG
EST: gi|162211065|gb|FC387089.1|FC387089
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162154402|gb|FC330209.1|FC330209
EST:     ATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: ATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162150060|gb|FC326591.1|FC326591
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162190967|gb|FC368373.1|FC368373
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162152471|gb|FC328034.1|FC328034
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGAAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|100390222|gb|BY952630.1|BY952630
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162175126|gb|FC351987.1|FC351987
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162169713|gb|FC345250.1|FC345250
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162158337|gb|FC334756.1|FC334756
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTC
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTC
EST: gi|162166434|gb|FC342416.1|FC342416
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGGAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGGAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
EST: gi|162164523|gb|FC341610.1|FC341610
EST:     CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAG                         GTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG
genomic: CTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTG

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: 65

CGGTTTCGAAGGAAACACTGGTGTGATTGTCATTGCTGCCACCAACAGGGCTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgtcat ... cgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG
                          tttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcatgaaaccatgatttaaatttgaacaatcttcaatcctcatggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacagGTTTCCGTGGATGTTCCGGACGTGAAGGGAAGGACTGACATCCTCAAGGTGCATGCTAGTAACAAGAAGTTCGCCGATGATGTGTCTCTGGATATCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT