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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtaagagctatcaatttctattgtttctaagttgcaacttccttttgccaagtttaaccttatatttctcgtcttcgattgttaattttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA

Basic information

species Physcomitrella patens
transcript PP1S100_191V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA08G26860.1 (Glycine max), 3'ss of exon 9
----gtatggtaagagctatcaatttctattgtttctaagttgcaacttccttttgccaagtttaaccttatatttctcgtcttcgattgttaat-tttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA
    ||   |  |||   || |     |||  ||| || | |  || ||  | ||  |   ||   | || ||    | ||  |   ||||||   |||   |||| ||| | || || ||||| |||  |||||  |||||| | |||||||||||||| |||||| | ||||||||||| |||||| |||||||||| ||||
tggggtggagccagatgaataataaaatataattt-tatgctagaatttggtattatct--ttctgcattttaaagattgttct-atttgttaccctttcttagGGGATACTTCATTCTGCTCTGCATAATGAATATTGGAGACTGATAGATCCTCAAGGGAAACCAACAGGAGTGATGGGATGGTGGGCTTCTCGTGCTGTTA

upper sequence: PP1S100_191V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv14s0068g00420.t01 (Vitis vinifera), 3'ss of exon 11
gtatggtaagagctatcaattt--ctattgtttctaagttgcaacttccttttgccaagtttaaccttatatttctcgtcttcgattgttaattttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA
 ||| ||      | |  | |    |  || | |||| |        | |  | |  | |||      | | |     ||  | ||  |    |||  ||||| ||| | || |  ||| | |||  | |||  ||||| || ||||||||||||||||||||| | |||||  |||| ||||||||||| || || || |
-tattgttgtttgtgtttagtgagttgatgatactaattcatgttaccttgctacataatttctttccaaaatcaaactcacctatgttattcttttccagGGGATACTCCATTATGCTTTGCATAATCAATATTGGAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCA
















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|162169840|gb|FC346196.1|FC346196
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|19780303|gb|BQ039545.1|BQ039545
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162166455|gb|FC342437.1|FC342437
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162167712|gb|FC344026.1|FC344026
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162245205|gb|FC422134.1|FC422134
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162171740|gb|FC348201.1|FC348201
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162254705|gb|FC430994.1|FC430994
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162169841|gb|FC346197.1|FC346197
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162164680|gb|FC340727.1|FC340727
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAN                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGA
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGA
EST: gi|162150065|gb|FC326596.1|FC326596
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|18338916|gb|BJ170942.1|BJ170942
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTTGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162171141|gb|FC347755.1|FC347755
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162164446|gb|FC341572.1|FC341572
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162183699|gb|FC359095.1|FC359095
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162164679|gb|FC340726.1|FC340726
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162171741|gb|FC348202.1|FC348202
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162167713|gb|FC344027.1|FC344027
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
EST: gi|162191939|gb|FC366944.1|FC366944
EST:     GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAG                         GGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT
genomic: GGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCT

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: 22 (upstream exon), 28 (downstream exon)
Score: 5

ATGCTCACAGACAAAGGATAGTGAATTGGATAAATGCTGCTGGTGGTACATCATCAGCATTTGACGTGACAACCAAGgtatggtaag ... attttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttgccaagtttaaccttatatttctcgtcttcgattgttaattttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA
                                        tgttaat  putative branch site (score: 5)
                                      attgttaattttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtaagagctatcaatttctattgtttctaagttgcaacttccttttgccaagtttaaccttatatttctcgtcttcgattgttaattttaacagGGCATATTGCACTCAGCTCTTCATGGTGAATTCTGGAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG