Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggagaggttaatggacttgttccttctgctcatctatgattgttgg...

Basic information

species Physcomitrella patens
transcript PP1S76_197V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA12G09300.1 (Glycine max), 5'ss of exon 1
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggaga-ggttaatggacttgttccttctgctcatctatgattgttgg
|| || ||   ||||   || || || || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||| || || ||||| |||  |||    ||  | || |   |||    |||   |   | | ||    | ||  |  |   | | ||  | |   || | |  ||  |    | |  |
CCCAACGTGAAGTGGAACGACGTCGCGGGGCTTGAGAGCGCCAAGCAGGCTTTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgaggattttgacttttcagttttttttttgtttgaacgattgaaggaactttgatgttgaacatttgaaatttaaattgttcgaatggaatggtttcag

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggagaggttaatggacttgttccttctgctc--atctatgattgttgg-----
|| || ||   ||||   || || || ||  | || || || ||||||||| ||||||| || || |||||||||||||||||||| || || ||||| |||      || |   | | | |  || |     |    |   || ||||    |  | |  ||       |   |  |||   |   ||   |  || ||||     
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgt------gagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 5'ss of exon 1
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactggg-agtggttctggagaggttaatggacttgttccttctgctcatctatgattgttgg-
|| |||||   ||||   ||||| ||||| || || ||||| || ||| | ||||||||||||||||| ||||| ||||||||||| || ||||| || |||             | | || |  ||     | ||| |  |    | || || ||  | ||      |  | | |   |  |    | || ||  |     
CCTAATGTGAAGTGGAGCGATGTGGCTGGGCTGGAGAGTGCGAAACAGTCTTTGCAGGAGGCAGTGATTTTGCCGGTGAAGTTTCCGCAGTTTTTTACTGgt--aatttgttgattatttgggactttgatttgatgttttttaatattgattttgtggtggaattgtggttagattggtgagaaagtgtaggaaagagaag

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ10867 (Selaginella moellendorffii), 5'ss of exon 1
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggagaggttaatggacttgttccttctgctcatctatgattgttgg
||  ||||   ||||   ||||| |||||| | || || ||||||||||| ||||| ||||| || ||  ||||||| ||||| ||||| || |||||||||| |   ||| |||   ||  |||   | || | |  | ||     |  || | ||   |  | |    || ||   |||  |  | |           
CCGGATGTCAAGTGGAGCGATGTGGCTGGATTGGAGAGCGCCAAGCAGGCTTTGCAAGAGGCGGTCATACTGCCCGTTAAGTTCCCCCAGTTCTTCACAGgttagt--gaatagcctact-tggt---agcgatgttcttctttttttctttttcgaagaggaagtaactttcttttctct-ttgctttgcag-------

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ25940 (Selaginella moellendorffii), 5'ss of exon 1
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggagaggttaatggacttgttccttctgctcatctatgattgttgg
||  ||||   ||||   ||||| |||||| | || || ||||||||||| ||||| ||||| || ||  ||||||| ||||| ||||| || |||||||||| |  |  ||    ||  |  |        |  |  |        |  ||| | |||||  | |   |||  |   |||  |  | |           
CCGGATGTCAAGTGGAGCGATGTGGCTGGATTGGAGAGCGCCAAGCAGGCTTTGCAAGAGGCGGTCATACTGCCCGTTAAGTTCCCCCAGTTCTTCACAGgttagtgaatagtctacttggtagcgatgttctctttctttctttcttttttccgaagagga-agtaaccttcctttctct-ttgctttgcag-------

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|162189692|gb|FC366330.1|FC366330
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGC
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGC
EST: gi|162243142|gb|FC416742.1|FC416742
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
EST: gi|162181631|gb|FC357933.1|FC357933
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
EST: gi|162154850|gb|FC331892.1|FC331892
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGNNNNNNNGGGACT
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCC-GGGACT
EST: gi|162149984|gb|FC326515.1|FC326515
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
EST: gi|208397729|gb|DC911980.1|DC911980
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
EST: gi|162229090|gb|FC404774.1|FC404774
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
EST: gi|162196819|gb|FC373887.1|FC373887
EST:     GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAG                         GGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG
genomic: GTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTG

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: 28 (upstream exon), 32 (downstream exon)
Score: 17

CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaaga ... tgaaatgcagGGAAGCGAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTGGAAAATCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATT




<











<


<