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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttggcaatgcttttcactcagaagttgaacatatg...

Basic information

species Physcomitrella patens
transcript PP1S32_182V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 5'ss of exon 8
-----------------------------GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggc-accatcta-ccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttggcaatgcttttcactcagaagttgaacatatg
                             |  |    |  | | | ||| |  ||||  | ||| |||||||||| ||||||||||| ||||||||||||||| || |  | ||   || |   ||  |  || | |    ||  || || | |  |  || |  | |    |||  |  |||||  |   |  || |    
AGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTATCTATGTTGGAGATGACAAGACTGATGAGGATGCATTCAAGgtaagccataaactggtctgcttgctcttacctgcaaaatatcaattactacttccatgtcttgatgt--ataatattgctcacttggc--tcaaatag---

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os04g46760.1 (Oryza sativa), 5'ss of exon 10
-----------------------------GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctacc--ttccacctggtgtcttctattgttctttttctgcat-tgagatcattcttttggcaatgcttttcactcagaagttgaacatatg-
                              | |  | ||| |  |   | |  ||||  | ||| |||| |||||||| || ||||||||||||||||||||   |    |  |    || ||       | ||  ||   ||||  |  |    | ||   | ||  ||   | | |||||   |   |  ||  ||      
AGCCGTCGAGTTTTTGCTTCGATCGCTTGAGCTAGATGATTCTGAAACTGTTCTTCCTATCTATATTGGGGATGATAAAACGGATGAAGATGCATTCAAGgtcacctttcttcagaaattgcataccacattttagatccatcttacttcgagcgttagtgaactcaattattattccttttttttttta--ttatacgaccag

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA12G00790.1 (Glycine max), 5'ss of exon 10
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttc--tgcattgagatcattcttttggcaatgcttttcactcagaagttgaaca-tatg------
|| |  |  ||    ||||| |  ||||  ||||| ||||||||||| ||||||| ||||||||||| ||||||      || ||  ||  |  || |||  | |   |  | | |||  || |||   | | ||  | ||   ||   ||| |  | ||  | ||||| | ||      
GGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaa----tatttaggtttaag-tgatgttgtgtggcgcacctattccctgtattttcacc-ttgctctgttgatttctttaatactgatatggaacaatctgttacag

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA17G14780.1 (Glycine max), 5'ss of exon 9
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacc-tggtgtcttctattgttctttttctgcattgagatcattcttttggcaatgcttttcactcagaagttgaacatatg----------------------------------------------------
||||    ||||  |||||| || ||||  | ||  | |||||||| || ||||||||||||||||||||||||  ||   |   |     |   | |  | |||  || ||  |||  |    |  | | ||| || ||  |     ||| ||       |||||| | |                                                     
GGTTAGCTGATAGGAATGATGTACTTCCCATTTACATCGGAGATGACAAAACTGATGAAGATGCATTCAAGgtattcaatttaagctgcgtaaaatagaattttcggttttttctttaatcggataggttaattattatgctacaaactttgacgattgcattgaactttttttagaatccaagagaaatatattatacattgaactatgttaactatatatag

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA06G47630.1 (Glycine max), 5'ss of exon 10
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtag----gcaccat---ctaccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttggcaatgcttttcactcagaagttgaacatatg-------
|  || |  ||    ||||  |  |  |  ||||| ||||||||||||  || |||||||||||||||||||||     |||  |     ||  ||  |  |  || ||   |||  |  ||||| |  |     ||  |||||||   ||    || |  | ||  |  |||  |         
GACTTAACAATTGCGATGACGTGCTAGCTATATATGTTGGAGATGATAGAACAGATGAAGATGCATTCAAGgtaataatgcataacttgttaattttgatgtcatgcctcaaatttcttgttttcagtttctctttccctcttttgtagatttccttaatactgatatcaaacggactgtaacag

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv00s0233g00030.t01 (Vitis vinifera), 5'ss of exon 9
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttg-gcaatgcttttcactcagaagttgaacatatg
|  |     |||   | ||| |  | ||| | ||| ||||||||||||  ||||||||||||||||||||||||    || |  | || ||   |||  |      ||| | |   | ||   |    | |  |   |    |||    ||     | |  ||   ||    
GACTAACCAATAGTGAGGATGTGCTCCCAATTTATATTGGAGATGATAGAACTGATGAAGATGCATTCAAGgtattacccgtgcaactgccttttgggttagggagttggtttggatgtgtgctactttgaggcaactacataatttgatttcactatatttttgtcag---

upper sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv02s0154g00110.t01 (Vitis vinifera), 5'ss of exon 9
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttg-gcaatgcttttcactcagaagttgaacatatg
|  |     |||   | ||| |  | ||| | ||| ||||||||||||  ||||| ||||||||||||||||||    || |  | || ||    ||  |      ||| | |   | ||   |    | |  |   |    |||    ||     | |  ||   ||    
GACTAACCAATAGTGAGGATGTGCTCCCAATTTATATTGGAGATGATAGAACTGACGAAGATGCATTCAAGgtattacccgtgcaactgcctttcgggttagagagttggtttggatgtgtgctactttgaggcaactacataatttgatttcactatatttttgtcag---

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|162268251|gb|FC444540.1|FC444540
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162152941|gb|FC329243.1|FC329243
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162172189|gb|FC348754.1|FC348754
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162151040|gb|FC326857.1|FC326857
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162187422|gb|FC362644.1|FC362644
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162156021|gb|FC332188.1|FC332188
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162163641|gb|FC340266.1|FC340266
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162197334|gb|FC372296.1|FC372296
EST:     AATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTTCA-G                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAG
genomic: AATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATT-CAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAG
EST: gi|162151213|gb|FC327693.1|FC327693
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162164955|gb|FC342146.1|FC342146
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
EST: gi|162173783|gb|FC349959.1|FC349959
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAG
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAG
EST: gi|162208296|gb|FC384400.1|FC384400
EST:     TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAG                         GTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC
genomic: TAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCC

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: 35 (upstream exon), 27 (downstream exon)
Score: 14

GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcacca ... taatttccagGTAGTCAATTCGACAAAATACGGCTGCAGTATTTTGGTGTCTTCTGTAGCCAAACCGACTGAAGCAAAATTTTCTCTCCGAGATCCATCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttctgcattgagatcattcttttggcaatgcttttcactcagaagttgaacatatg

- - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG