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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA

Basic information

species Physcomitrella patens
transcript PP1S207_36V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttg--gttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
| |  |  ||   | |      |  || |    ||  |  | |  |     || |    |   |  || ||  ||     |  | |||  | |  ||   |||| ||||| || || || || |||||  |||||||||| ||  | ||||| |||||||| ||||| |||||||||||||||||||| || ||||| || |
tacagttcatcc-tcctgacagactttgtgctcatatatctgcactacacatgtatttggtgcttatgatgcagtaacacatagtatttttctaattt-tagGTGTATGGTTTCTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
tgccatatatttatgcatg-tgaaagttatctgaattcaattactttttgtgtgg-accatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
||| || | | ||| |||  || |    |  ||  |  ||  ||||    |||   | | |   ||| ||      |   |   |  ||   | |     |||| ||||| || ||||| || || ||| |||||||||| ||| | ||||| |||||||| ||||||||||||||||| |||||||| || ||||| || |
tgc-atgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcct-tagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 4
----tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
    | |   ||    ||     |    || ||   ||  | |  | |      ||     |   | |  ||||  ||||| |   | ||  ||| ||||  |||| |||||||||||||| ||||||||| |||||||||| ||  | |||||||||||||| || || ||||| ||||||||||| || || || || || |
ataattcataatggagatatgaattgtggtaatactaaaactagaaatgcccaagtatcatactgatttatgttaattttgta---atttactgt-tttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTACCTAACTCTTTCTGCAATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgt-ggaccatgaaatgttgttggttttgaacggaattg-gtgtgtttgac-agGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
    |||   |  |   |||||||||   || |  |     | | |   ||| | |   |   |||    |   | | ||     |    | |||||  | |||| |||||||||||||| ||||||||| |||||||||| ||  | ||||||||||| || || || |||||||||||||| ||||| || || || || |
--agataaggtattaattgtgaaagt-gcctaagattggaaattataaatgttgaattctagtatgccactttatgttaatattgtaatatatgtttttctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGGAATGCTAATGCTTGGCGATATTGTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgt----ggaccatga--aatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
    || |  | ||| |  |   | || |   ||| | |  ||      ||     | | |||||  | |  ||||  ||||| |   | ||  ||| ||||  |||| |||||||||||||| ||||||||| |||||||||| ||  | |||||||||||||| || || ||||| ||||||||  | ||||| || || || |
--agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgta---atttactgt-tttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttg-ttggttttga--acggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
      | | | | | |  |   | || |   ||| | |  ||      ||   |   |   ||| || ||  | || |  | | ||||      ||||  |||| |||||||||||||| ||||||||| |||||||||| ||  | ||||||||||| || || || ||||| |||||||| || ||||| || || || |
-attcaaaagtaaggta-atattaattgtggaaatactaaaaccagaaatgcaaaa-gtatcatgctgatttatgttaattatgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGCTATTGTACAGATGTGTTTGACTATCTAACACTTTCTGCAATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 4
tgccatatattt-atgcatgtgaaagttatctgaattcaattactttttg--tgtggaccatgaaatgttgttggttttgaacggaattggtgtg-tttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
    ||  ||||  || || ||     ||  |||    |||||    | |  | | |||  |||| |  | |         |   | ||| | |  |||   |||| ||||| || ||||||||||||||| |||||||||| ||| | ||||| ||||| || ||||| |||||||||||||| ||||| || ||||| || |
----atgcatttcgtgaatctgctgactagatgatcaaaattatacatggattctcgacattgaactcctttataacacagaaccatttgatttacttttttagGTGTATGGTTTCTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatc-tga-attcaattactttttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
   |||  | |         |||  || |  ||| |||   |  | |   |  |      |  | | || ||   ||        | |  | | ||||  |||| ||||| || ||||||||||||||  |||||||||| ||  | ||||||||| | || ||||| |||||||||||||| |||||||| ||||| || |
--acatccactgtcaaggacgaagattgtagtgatattttgtgccctgcaggttcatttttatagttttcttaaattgtcgtaccaattttatatttgctagGTGTATGGTTTCTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttggttttgaacgg-----aattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
    |  | |||   ||  |   | | |     |||  |  ||| |       ||      ||| ||   | | || |   |     | ||    | |||  ||||| ||||| || ||||| || |||||| ||||||| |||||  | ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||
----aactgtttccccacatagga-tgaaacacattgcacaactgtgacaagagatttaccaatatttaggatatttattagtgtatacttttcttcttttccagGTCTATGGTTTCTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ25636 (Selaginella moellendorffii), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
             ||  | |  || || | |   || |   ||||||  | |   | | |||| |   ||  |||| ||||   |   || | ||  ||||| ||||| || ||||| |||||| |||||||||||||||| ||||| |||||||| ||||| ||||| ||||| || || || ||  |||| || || |
------------gtgattctcgaattttttt---ttaagaaacttttgttctccccaacgaaaagaattttttttttaacgcgttgtttgagcttc-cagGTGTATGGTTTCTATGATGAATGCGAGCGGAAGTATGGAAATCCAAACGCTTGGCGTTACTGTACTGACGTTTTCGATTATCTAACTATCTCTGCGATCA

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ05314 (Selaginella moellendorffii), 3'ss of exon 4
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
             || ||     | || | | ||   ||  ||||||  | |   | | |||| |   |   |||  ||||   |   || | ||  ||||| ||||| || ||||| |||||| |||||||||||||||| ||||| |||||||| ||||||||||| ||||| || || || ||  |||| || || |
------------gtg-attctcgatttttttaaa---aaaaacttttgttctccccaacgaaaagaattatctttctaacgcgttgtttgagcttc-cagGTGTATGGTTTCTATGATGAATGCGAGCGGAAGTATGGAAATCCAAACGCTTGGCGTTACTGCACTGACGTTTTCGATTATCTAACTATCTCTGCGATCA

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|208390402|gb|DC933447.1|DC933447
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATA-CTCAG                         GTATATGGATTTTATGACGANTGCCAGCGNA-GTATGGAA-CCCAA-TGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|100389837|gb|BY971189.1|BY971189
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTA
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTA
EST: gi|100386396|gb|BY951192.1|BY951192
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|162174230|gb|FC350613.1|FC350613
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|100381804|gb|BY950182.1|BY950182
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|208389011|gb|DC937344.1|DC937344
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAA-CCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|208390592|gb|DC937524.1|DC937524
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|100352556|gb|BY945331.1|BY945331
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|100353825|gb|BY983329.1|BY983329
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT
EST: gi|208387516|gb|DC933379.1|DC933379
EST:     CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG                         GTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAA-TGCT
genomic: CTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCT

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: 22 (upstream exon), 29 (downstream exon)
Score: 10

ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAGgtattgactt ... tgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgtggaccatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA
            atgaaat  TA-rich tract