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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat...

Basic information

species Physcomitrella patens
transcript PP1S220_79V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA08G03690.1 (Glycine max), 5'ss of exon 1
-----------------CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatc-attctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat--
|||||| | |||||||||||| | |||||| | || |||||||| ||||||||||||||||| |||||| | || ||| | ||||| || | || ||| ||| ||||| | || |||| || ||| | || || | | | || | | | | | | | | |||||||| |
GAAACTGAGACGTTTGCTTTCCAGTCCGAGATCAACCAGCTCCTTAGTCTTATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTTAgtgagctcatcagcaatgcctctgatttaagattctt---atattatagggttcatgtttatcatactctgtttttccattgttgctccgtaacataacgtccctgtattgtgagaattatgtgggtag

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaa--ttttctttaaactt-ttgcaagttcttgaatatttgaatcattctcagttgatctatcagggt-cgcattgcg-ctttaagtctgagaattccagacat
|| ||||| |||||||||||| | || ||| | || |||||||| ||||||||||||||||| || || | | ||| | ||||| || | || ||||||| ||||||| ||| || | |||||| | | ||| ||| | | || | |||| || | || | | || ||| |
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtctt--ttggtatttccatttgttcattacgtcctttactgcgatcgttcttta---

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaat-tttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat
|| ||||| |||||||||||| | || ||| | || |||||||| ||||||||||||||||| || || | | ||| | ||||| || | || || |||| ||| | | | ||| || || || | || || ||||| | || | || | | | |||
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca-

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
-CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcatt--ctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat
|||||||| |||||||||||| | || ||| | || |||||||| |||||| |||||||||||| ||| | | || | ||||| ||| | || ||||||| |||||| ||| | ||| | | ||| || || || | ||| | ||| | || | | || | | |
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcctttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttc--atccaattta-

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA08G44590.1 (Glycine max), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatca--ttctcagttgatctatc-agggtcgcattgcgctttaagtctgagaattccagacat-
|||||||| |||||||||||| | || ||| | || |||||||| |||||| ||||||||| |||||| | | || | ||||| ||| | ||||||||| |||||| ||| || | ||||| | ||| || || | |||| | | | | || | || ||| | || || ||
TTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAGATTTTCCTTCGTGAACTCATCAGCAACGCCTCCGATgtacgtttcttcgt-ttttcgc---tccttgacttgttgtttctgcttgtttcgtgatgtgtttatgttcttcatccgattttattcaactaacatgctttatt

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv00s0194g00030.t01 (Vitis vinifera), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctg--agaattccagacat--
||||||||||||||||||||| |||| ||| | || |||||||||||||| ||||||||||| |||||| | | ||| | ||||| || || |||||||| | ||| || ||| | | ||| || || | || || | || || | || | || | | || | | |
ATTCCAGGCGGAGATCAACCAGCTGCTCAGTCTCATCATCAACACTTTCTATAGCAACAAGGAGATTTTCCTTCGTGAGATCATCAGCAATTCCTCCGATgtgagttttcagaacagtttctccttcacttctccttttaaggatct--gatcga-ctgcgtgtgttgcgc-gtatttcatgttcgtaatgatgcaatgcgatt

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat---
|||||||| ||||||||||| | | |||||||| |||||||| ||||||||||||||||| ||||| | | ||| | ||||| || || || ||||||| | || || ||| | || || | || ||||| | | || | ||| | | ||||| | | |||| | | |
TTTCCAGGCTGAGATCAACCAACTCTTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTTCTCCGTGAGCTCATCAGCAATTCCTCTGATgtaagtc-ctatactttttatctttttttttcctcatttaatcagtttttttttcgcgatcctgttttatttgcggctga--tctgttctctgttggtttatt

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaatt-ttctttaaacttttgcaagttcttgaat---atttgaatcattctcagttgatctatcagggt--cgcattgcgctttaagt-----ctgagaattccagacat
|||||||||||||||||||||| | || ||| | || |||||||| ||||||||||||||||| || ||||| | ||| | ||||| || | || ||||| | | || | | || | | || | | ||| ||| ||| | | | | | || | |||| | ||| || ||||||
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcattctttctgcgatttccag----

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ29061 (Selaginella moellendorffii), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat
|||||||| |||||||||||| | || ||| | || |||||||||||||||||||||||||| |||||||| | ||| | ||||| || | || ||||| | | | || ||| | | | | ||| | ||| || ||| | | || | | ||
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtat-ttcgcctccttgt---tcttccagttcttgtcaaactctttcttcttctcatgctgcgccgctgtgactccag------------------

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaatt-ttctttaaacttttgcaagttcttgaat---atttgaatcattctcagttgatctatcagggt--cgcattgcgctttaagt-----ctgagaattccagacat
|||||||||||||||||||||| | || ||| | || |||||||| ||||||||||||||||| || ||||| | ||| | ||||| || | || ||||| | | || | | || | | || | | ||| ||| ||| | | | | | || | |||| || ||| || ||||||
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcgttctttctgcgatttccag----

upper sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaac-ttttgcaagttcttg--aatatttgaatcattctca-gttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat
|||||||| |||||||||||| | || ||| | || |||||||||||||||||||||||||| |||||||| | ||| | ||||| || | || ||||| | | | | | || | | |||||||| || | | | |||||| | || || | ||
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag-----------------------------

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|18367980|gb|BJ200064.1|BJ200064
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18330761|gb|BJ162767.1|BJ162767
EST:     ACAGCAACAANGCAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18349621|gb|BJ181671.1|BJ181671
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|67712633|gb|BJ966082.1|BJ966082
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|67578554|gb|BJ950721.1|BJ950721
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|67712759|gb|BJ966208.1|BJ966208
EST:     ACAGCAACAANGAAATTTTCTTAAGANAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|67575001|gb|BJ947825.1|BJ947825
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18357655|gb|BJ189714.1|BJ189714
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18342532|gb|BJ174567.1|BJ174567
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18347003|gb|BJ179049.1|BJ179049
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|162178680|gb|FC353949.1|FC353949
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGCAAGATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18326411|gb|BJ158410.1|BJ158410
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18363241|gb|BJ195313.1|BJ195313
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|162197953|gb|FC373981.1|FC373981
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGCAAGATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|67575021|gb|BJ947845.1|BJ947845
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
EST: gi|18349581|gb|BJ181631.1|BJ181631
EST:     ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGAT                         GCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT
genomic: ACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGAT

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: 20 (upstream exon), 35 (downstream exon)
Score: 17

CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttct ... aatatggtagGCCTTGGACAAGATTAGGTTTGAGTCCCTGACCGACAAGAGTAAAATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA