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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG

Basic information

species Physcomitrella patens
transcript PP1S307_16V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os10g03400.2 (Oryza sativa), 3'ss of exon 3
-----tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctt--tatatcacgattcttattcgcaagttgtgattcgttcgt-----------tcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
     | | |   || | |   ||  |   | |  ||| |  ||    ||   ||     ||  || ||  |  |  ||||  |||  |      |  ||| |           |||||| ||  |||||  ||||  || ||| |||    | | |||||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||| || |||
gtaattgcatctatcaa-ataggttaaggttaaactatatttggactaatccttttatggttgatacatacctttgtttataagcagttgacacatttttcatcaaattctatctcagGATTTTGAATTTGAAGAAGCTGGCAAGGTGGCAGAATGCTATCCTCAAGGTTATCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGACTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 4
-tacgtgcttc-gacaccagtacat----actgatttatgtgaggg-ggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
 ||  |||||  ||    | || ||    ||| ||   | |  ||  | || |||   | | ||||||   |  ||   |        ||   || |  ||  |||||| ||  |||||  ||||  |||||| |||    | | |||||||||||| || |||||||| ||||| ||||| |||||||| ||||||||| |  |||
gtaattgcttaagattaaaatatatttggactaatccttctatggttgacacataccct-tgtttataa-gcagttgacacatttttcttcaaatcctatc--tcagGATTTTGAATTTGAAGAAGCTGACAAGGTGGCAGAATGCTATCCTCAAGGTTACCATGGGGTTGATAAGGAAGGAAGGCCTGTCTACATTGAACGTCTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 4
tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttata---tcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
 |      |  |||  |      |   || |  |  |      | |   | |   || |||   |   |   | | |||      | | || |  ||  | |||| ||| ||||   ||||  ||| || |||    | | ||| |||||||| || |||||||| ||||| |||||||||||||| ||| ||||| |  |||
-atacatatacacaaaaaagagaagcaatcttaggaattatttacaggctattagttcataaacttttgtaaccttttccttttctctaatgcaatc--ttagGAATTCGAATTCGAAGAAGCTGATAAGGTGGCAGAATGCTACCCTCAAGGTTACCATGGGGTTGATAAGGAAGGCAGGCCTGTCTACTTTGAACGGCTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
------tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
      |   |  |||  || ||| | ||  |    ||||  ||  | ||  |  ||| | ||| |||   | || |  |  |   || |||||   |   |  |||| ||  |||||  |||  | ||  ||||   | | || |||||||||||||| ||||| || ||||| ||||| ||||| || |||||||| ||| |||
aatctttgaatatttcagcatcagcatatttt---ctatgctagaagacaccttatgtatgttt-tattttgctt-tggtgtgattgtggtgata-atgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
----tacgtgcttcgacacc-agtacatactgatttatgtgagggggcatatattgtctctttatatca--cgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
    |    | ||| | |   || ||||  || | ||||  |||  |||  |  |   |  ||   |      | ||| ||  |   ||| |||  | || |   |||| ||  |||||  |||  | ||  |||||  | |  | || ||||||||||||||||| || || || ||||| ||||| || |||||||||||  |||
tgtttgtacgtttcaaaatttagaacatg-tgttctatgctaggatgcacttgatacatgatttggttggttaagtctaat--gtctgttctga--catttga--agGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 4
--tacgtgcttcgaca-ccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
  ||  |||||    |  |  |  ||| |  |     | ||      |  | ||       | | |  ||| | | ||      | ||     |||  |  |||| ||  |||||  |||  | ||  ||||   | | || |||||||||||||| ||||| || ||||| ||||| ||||| || |||||||| ||| |||
attatttgcttttttaatctttgaatatt--tcagcatcagcatattttcaatgctagaagacaccg-gatacatgttttattttggttgggtgtttttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTTTACATTGAGAGACTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
tacgtgcttcgacaccagtacat-actgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgtt--cagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
                 ||  || ||   ||| |   |     | ||   |||  ||||  ||| |   |  |  |   ||  |   ||  ||  |||   |||| ||  |||||  |||  ||||  ||||   ||| ||||| ||||| || |||||||| || ||||||||||| |||||||| |||||||||||| | |
-----------------gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaatct-caatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------tacgtgcttcgacac-cagtacatact-gatttatgtgagggggcatatattgtctctttatatca--cgat----------tcttattcgca-agttgtgattcgttcgtt-----cagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
                                                      | ||  ||        |  ||||||| | | | ||   |   |||| || |   ||| |  || |   |||          ||| | ||  | | || |  |  ||  ||       |||| ||  | ||   |||  ||||  ||||   | | |||||||||||||| |||||||| || ||||| ||||| || ||||| |||||||||||| |||
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
                |  | |||  | || |  || ||   || |  | ||  | |  |     |   || |    ||  ||   | | | |     |||| ||||| || | |||  | ||  ||||||  |   |||||||||||||||||||||| || |||||||| || || ||| | || || || ||| |||
--------------gtacgagatatggtttcagctgtggtttcaga-gtagtagcatcttgctgtggaactaaca-acattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG

upper sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G16380.1 (Arabidopsis thaliana), 3'ss of exon 4
--tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgtt----cagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
  ||  |  ||   ||  | |        || |  |   |      |||||   | |  | | | |||| |  | |       || | |||  ||   |     |||| ||| | |||  ||| || ||  ||||    ||  | ||||| ||||| || ||||| ||||| |||||||||||||| || |||||||| ||| | |
gttaactttttgtccaagaatcttggaacatcttagactgatcatttatatatacacaatctttgacgagtgatttgtttggtttataatttttttaataatgaagGATTTCGAGTTTGAAGAGATCGATCAAGTACTCAAACATTATCCGCAAGGTTACCATGGAGTGGACAAAGAAGGCAGGCCGGTTTACATTGAGAGATTAG

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|162254955|gb|FC431140.1|FC431140
EST:     AAAACATGTTAGCTTGGCGCATGGAGTTTGGGACAGATACAATTGATGAG                         GACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGG
genomic: AAAACATGTTAGCTTGGCGCATGGAGTTTGGGACAGATACAATTGATGAGgtttgtatta ... gttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGG
EST: gi|162255006|gb|FC430879.1|FC430879
EST:     AAAACATGTTAGCTTGGCGCATGGAGTTTGGGACAGATACAATTGATGAG                         GACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATC
genomic: AAAACATGTTAGCTTGGCGCATGGAGTTTGGGACAGATACAATTGATGAGgtttgtatta ... gttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATC

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

GTTTATCAAGGCAAGAAAATATGATGTCAAGAAAGCAGCAGAGATGTGGAAAAACATGTTAGCTTGGCGCATGGAGTTTGGGACAGATACAATTGATGAGgtttgtatta ... gttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
                                          ttcgttc  CT-rich tract
        tctttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA