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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcataaaacattgttgatctccaagttccataaataacttgttttcagctatttggataatcgctatagcgaataatacgatgataatttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT

Basic information

species Physcomitrella patens
transcript PP1S8_105V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
tctcataaaacattgttgatctccaagttccataaataacttgttttcagctatttggataatcgctatagcgaataatacgatgataatttt--tttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT
|   ||  |       | || |   | ||   | | | |    ||     |  | ||  || |     ||    |   || |   ||  ||     || |||||||||||| ||||||||||||  | |||||||| || |||||||||  |||||||||||| | ||| || ||||| ||||| ||||| || || ||| |
tagtattgacagcgtcttatttgtgactt--gtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G883149_T03 (Zea mays), 3'ss of exon 2
tctcataaaacattgttgatctccaagttccataaataacttgttttca-gctatttggataatcgctatagcgaata-atacgatgataatttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT---
   |||||   | |  |||     | ||    | |    | ||||| |  | | |||   |  |     ||    |||  |    |  |   | |||  |||| ||||||| ||||||||||||  | |||||||| ||||||||||||  |||||| || || | ||| || ||||| || || ||||| || || ||| |   
---cataatgaactcatgagtgtgatgtat--tgatgtgcctgtttgcgtgttttttcttttcttcaagtatttcatatgtttatttgtttctctttaacagcagAGATTGTAATGTTTGATGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAGGAGAATGAGCTTATTTTAGC

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G883149_T04 (Zea mays), 3'ss of exon 2
tctcataaaacattgttgatctccaagttccataaataacttgttttca-gctatttggataatcgctatagcgaata-atacgatgataatttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT
||||||||   | |  |||     | ||    | |    | ||||| |  | | |||   |  |     ||    |||  |    |  |   | |||  |||| ||||||| ||||||||||||  | |||||||| ||||||||||||  |||||| || || | ||| || ||||| || || ||||| || || ||| |
tctcataatgaactcatgagtgtgatgtat--tgatgtgcctgtttgcgtgttttttcttttcttcaagtatttcatatgtttatttgtttctctttaacagCAGAGATTGTAATGTTTGATGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAGGAGAATGAGCTTATTTT

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|18348987|gb|BJ181036.1|BJ181036
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|19790513|gb|BQ041913.1|BQ041913
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|208382534|gb|DC919758.1|DC919758
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|162221832|gb|FC398399.1|FC398399
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|22491811|gb|BU051734.1|BU051734
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|18339333|gb|BJ171360.1|BJ171360
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|162222858|gb|FC399320.1|FC399320
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|208348631|gb|DC905868.1|DC905868
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|162221833|gb|FC398400.1|FC398400
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|18363484|gb|BJ195556.1|BJ195556
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTC
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTC
EST: gi|22492703|gb|BU052626.1|BU052626
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|37840617|gb|BJ598625.1|BJ598625
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|37834059|gb|BJ592071.1|BJ592071
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|162222859|gb|FC399321.1|FC399321
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|7286949|gb|AW599436.1|AW599436
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|67507871|gb|BJ940747.1|BJ940747
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
EST: gi|37835955|gb|BJ593967.1|BJ593967
EST:     TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAG                         CTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG
genomic: TGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAG

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: 31 (upstream exon), 32 (downstream exon)
Score: 11

GTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATAAATTGGCGTATGAGAAATCCGTGTTCACGAAAACCCAACGCTCGATTGCCCGCTCAGAAGgtatgatcta ... ttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagctatttggataatcgctatagcgaataatacgatgataatttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT
                                            tttttttgc  CT-rich tract
                            aataatacgatgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcataaaacattgttgatctccaagttccataaataacttgttttcagctatttggataatcgctatagcgaataatacgatgataatttttttgcagCTGAGATTGGAATGTTTGATGGATATATTGTGGTCTACAAGTTCATCTCAGACCTCCATTTCTATGTCACGGGAGGTGAGGATGAGAACGAACTGATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG