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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtatgttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA

Basic information

species Physcomitrella patens
transcript PP1S8_312V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
--------------------------atttttcaatgt-ttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgt-ttgtatgttgatccactccgttttc------ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
                            ||   ||||| ||||  | ||    |   ||||||||  |  ||||  |   || || || | | |  ||| |||        | | | |      |  ||| |||||| | || ||||| |||||||| || || || ||||| || ||||| |||||||| || || |||||||| ||||| || ||||||||||| || ||||
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttc-ctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtatgttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
             ||   ||   ||||   || |    || |  ||||   |  | | ||    ||  |   || ||    || |||||     ||||||||| |||| ||||| || || || || || || || || || ||||| ||||||||||| || |||||||| |||||||| |||||||||||||| || |
------------gtaaactcagttgttaccaagt-gtctcctccatgatctaattgtgatagccttcatgc-ttaatgacttctgtttt-----ttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtat-gttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
               | ||     | ||  ||||    | |  |  | |  ||  ||     |   ||| | | ||||   ||   ||||||  ||  |||||| |||| ||||| || || || ||||| || || || |||||||| ||||||||||| || || ||||||||||| ||||| |||||||| || || |
--------------gtgattactcgatt--aattcttcttacagtggtgatagtcatttgaatacatgtgttgctgatt-gctttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 9
atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtatgt-tgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
             ||     | ||||   |  ||||   |||  |||| |   | ||  ||   |  |||| | ||||  |||   ||||   || |||||||| |||| |||||||| ||||| || ||||| || || || |||||||||||||| || || || |||||||||||||| || ||||| ||||| || |
------------gtaatgcatcctgtcaagg-tttagcccatacatgact--accattttgaaatgggtatttctgat--actttcttttgtactctacagCGTGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCA

upper sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 8
atttttcaatgtttatcatcttctgttttgaatttaattcatggatgagtcagctatcatgctgtttgtatgttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
                                              |  |  |  ||  |  |||     |   | |  |||    |||||   |||||||| ||| |||||||||| ||||| || || || || || |||||||| ||||| || || || || ||||| || || |||||||||||||| || || |
----------------------------------------------gtatgtgaaattttattgtcgagctagagctgaactggcctttcc---ttacagCGCATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

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|100398889|gb|BY990566.1|BY990566
EST:     GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAG                         CGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT
genomic: GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAGgtacggtcag ... ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT
EST: gi|162149955|gb|FC326278.1|FC326278
EST:     GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAG                         CGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT
genomic: GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAGgtacggtcag ... ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT
EST: gi|162154257|gb|FC330388.1|FC330388
EST:     GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAG                         CGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT
genomic: GGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAGgtacggtcag ... ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATT

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: 8 (upstream exon), 32 (downstream exon)
Score: 2

GCCTGGCCTGTCCGTACACCACGGCCTGTTGCGGAGAAGCTCGCCGCTGACACTCCCTTGCTCACGGGCCAGgtacggtcag ... ccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtcagctatcatgctgtttgtatgttgatccactccgttttcccctttacagCGTATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAA
                         tgttgat  putative branch site (score: 2)
                               tccactccgttttccc  CT-rich tract
                   tttgtat  TA-rich tract