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

...cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
---cgtcatagtcctttttaattttagttattttt--taatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
        |   |  | |  | |  | || ||  |   |  || | || |      ||| |     |   ||||| ||   ||        | |  |  | ||||||||  |||| |||||||||||||||||||| ||||| || ||||| |  |||||||| || || || |||  |||||| ||| | || |||||||||||
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccattag---atactatcgttctaaaccaggcat--gtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
cgtcatagtccttttt--aattttagttattttttaatttttagt-tttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
 ||| |  | |||||   ||| |      | |    ||| |  || |||||   ||| || |   | || ||  |  || || |      ||||  |   |||| ||| ||||||||||||| || || ||||| ||||| || ||||||||||||||||| || |||||||||  |||||| ||  | || ||  | |||||
ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgtctttgacagattagtttttttgttggtcct--ctgatatagtatgtttg-atggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
------------------------cgtcatagtcctttttaattttagttattttttaatttttagttttgagttatt-cgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
                        | |||| ||  | | || ||   ||     |   ||   || |||||| |  ||  || | |||  || |  || ||  | |   ||||   |  |   ||| ||    ||   |||||| || || ||||| ||||| || |||||||||||||||||||| || |||||| ||||||| || || || ||  |||||||
gttaatacccctgaagtttttattcttcat-gtattgtgtatttggggtggcaataatatacata-ttttgactggttatgtttaaattgtcttctta-cttgtatttggattg-atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
-----------------------------------------------cgtcatagtcctttttaattttagttat----tttttaattttta---gttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
                                                |  ||| |    || | |||   | ||    | |||   ||||     |||||| |  ||    | || ||   || |  ||  | |   ||||   |  |   ||| ||    ||    ||||| || || ||||| ||||| || |||||||||||||||||||| || |||||| ||||||| || || || ||  |||||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgttttgcttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattg-atccttttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 11
-cgtcatagtcc---tttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
      | | ||    | | |||||  |    | | ||  |   ||  ||  | | ||  ||   |   |  || | | | | ||   | | |  | |   |||| |||   |||||||| || ||||||||||| |||||||| || ||||| || ||||| || ||||| ||| ||||||| ||  | || || || |||||
tttctttggaccaagatatgaatttctgcagatctctacatacaagcattctgctgttgcta---actctgatttttggtga-cttgtggtctaatttatgcagGCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACTTCAATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 13
cgtcatagtcct---ttttaattttagttattttttaatttttagttttgagttattcgta---tgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC-
    | | |||    | | |||||  |    | | ||  |   ||  ||  | | ||  ||     ||| || |  ||  ||  | | |  ||||  ||    |||| |||   |||||||| || ||||||||||| |||||||| || ||||| || ||||| || ||||| ||| ||||||| ||  | || || || ||||| 
accaagaatccaatatatgaatttctgcagatctctacatacaagcattctgctgttgctaactctaatttttg--gtgacttgtattctaattt-atg----caggCACACAGTATACACAACAATCATACAAAGTAAGTGACTCATTCCCATTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTGACCTCAATGGCC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
-----cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaac-----agGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
          |  || |   || ||||    | |||     || | || ||    || || | ||||| |  |   ||    || |   | |||    | ||      ||| ||    |||||||||||||| |||||||| || || || || || || |||||||| || ||||||||| ||||||||||| | || || || |||||
gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtc-tctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
----------------------------------cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
                                   |||| |       || | | |||  | | |   | ||| | | |     |||      || ||||| ||     |  | | |   || |   ||   |||||| || ||||| ||||| || |||||||| || ||||||||||| || |||||||| || |||||||||  |||||  ||| | || || || ||| |
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
cgtcatagtcctttttaattttagttattt--tttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattt-tgtgt-taacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
      ||||   |  || |||  | ||    |||||| ||    | |    ||||  | ||| |   |      | | || |   | ||| ||| | |   ||||||  | ||||| ||||||||||||||||||||||| || ||||| ||||| ||||| |||||||| |||  |||||| ||| | || ||||||||| |
----tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
cgtcatagt--cctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
 ||||  ||  | | |||||    | | ||||||| |      |  ||   ||||   | | |    ||  | |    | |||    ||||  ||   | ||| ||   ||||  ||||||||| || ||||| ||||| || ||||||||||||||||| ||||| |||||| |||| || ||||| |||||  |||||||
-gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgttatctgtctcttttaacc-tctgttaatttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC

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|162165498|gb|FC340609.1|FC340609
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|162228109|gb|FC405691.1|FC405691
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|162191374|gb|FC367130.1|FC367130
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|162185156|gb|FC362290.1|FC362290
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|162176694|gb|FC352539.1|FC352539
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|100448451|gb|CJ972750.1|CJ972750
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|37831666|gb|BJ589678.1|BJ589678
EST:     TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: TGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
EST: gi|162157367|gb|FC333170.1|FC333170
EST:     CTTGGTCGTCATGTCTAAAG                         GAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA
genomic: CTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTA

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: 33 (upstream exon), 35 (downstream exon)
Score: 6

GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgtatttcacc ... gtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
           tatgaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtcatagtcctttttaattttagttattttttaatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA