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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC

Basic information

species Physcomitrella patens
transcript PP1S66_174V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                         |   |||  ||   || || |      |||  |   |    |  ||| ||     || |       ||| ||     || | || ||  ||||||||||||||||||||| || || ||||||||||| ||||| || | ||| ||| |
----------------------------------------gtgagtttactgaagttaataacc----attctatgctgccatg-gagctcaa---cgtatcttgacttaatc-ttaattaaaatttt--ccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 4
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccg-ttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                      | || ||   ||  | ||||| || | |       |   |||| |    |  || |||| ||||   ||| ||| ||  | || ||      |  |||| ||||||||||| || || ||||||||||||||||||||   |      ||  |
-------------------------------------gtaat-gacacctcat-tttgactactacgagagaaactgttttctttttgccct-ttccaaaat---tttaattaacttggtttatgaaaaatgtagGTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACAC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccg-atttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                      ||| | ||   |||   || |  ||  | | || ||    |||  |    ||| |||   | || ||| | ||||                   ||||||||||| ||||||||||| |||||||||||||| ||||| |||   || ||   
-------------------------------------gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatattt------------------cagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 4
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACT-CTTCAGGCCAGGC--
                                |  |||| |   |||| ||    | ||| |   | ||   ||   || ||     ||| |||        |  ||||  | |   | || |      | |||||||||||||||||||| || ||||| ||||| ||||||||   |  ||  ||   |  
------------------------------gtatgtgctcacgaattttttaa--tagatgaa--cggaacagaggcttgtg-----gttgtctct----gcatgttttggtaatgaggtgttgc---atacagGTCATGGATATGCTTGGCCCTAGTCTGTGGGACGTTTGGAATAACAACAATCCTCACAT

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                         ||   || | || |  |  || || |   |||| ||    | |  || | ||||    |||  |        |  | || |||  |  | ||||||||||| ||||||||||| || ||||||||||||||||| ||||  |  ||  |
----------------------------------------gtaagcttttcgtatgagcctagtcacacattgagat----gaatcaggtatcttt---aatgaag-------aaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                         ||  |   ||    |    | |     || |  | |||   ||    || | ||   |  ||||    | | |  |  | |||| |  | ||||||||||| |||||||| || ||||| |||||||||||||| ||||| || ||  |
----------------------------------------gtatgtaatttacaatgagctttgttaaatat--actttcgatattgattgtgttatcatgtaca----agtaatgctataatatatacttcagGTCATGGACATGCTTGGTCCGAGTCTCTGGGATGTTTGGAATTCTTCGGGGCAATC

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 5
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                           || || | || |   ||| |||   ||  | | ||      | | ||    | |  | |     | | | |         | | |||| |||||||||| ||| | |||||||||||||||||| ||||||| |||  ||||||| |
-----------------------------------------gtgagttttggtttgaaattgttcatcatcaggacttc-----caaatt----tacacattgtgcctgaattaaataaaataaacatgtc-agGTCATGGACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC

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|162165455|gb|FC342022.1|FC342022
EST:     GGGTTCCTCGCGTGCATTACAAAGGCCGTCAAGGGGATTACTACGTCATG                         GTCATGGATATGCTTGGGCCAAGCCTTTGGGATGTTTGGAACTCTTCAGGC
genomic: GGGTTCCTCGCGTGCATTACAAAGGCCGTCAAGGGGATTACTACGTCATGgtgggctatt ... tcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGC




















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: 21 (upstream exon), 28 (downstream exon)
Score: 3

CACTCTTGGTGGCAGTCATGGGGTTCCTCGCGTGCATTACAAAGGCCGTCAAGGGGATTACTACGTCATGgtgggctatt ... tcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC
                                     cgttgat  putative branch site (score: 3)
                                             tcttgtcc  CT-rich tract
                   aaatacattttattca  TA-rich tract