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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC

Basic information

species Physcomitrella patens
transcript PP1S318_21V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 4
aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                  | | |   ||    || |  |  |  |   || |     |  |      || | |  ||| |||  | |      ||  |||||||||||||||||||||| |||||||| || |||||    ||||||||||| ||  | || ||||| ||||| ||| | ||  | |||||  | |||  
-----------------gttagttgatcccctgaccagtctagctgccatttagttgc--atccaacatcctaacgtgcttctgttt------tcaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAAGA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                  | | |   ||    ||    |  |  |  ||| |     |  |      || | |   || |||  |         |  |||||||||||||||||||||| |||||||| || |||||    ||||||||||| ||  | || ||||| ||||| ||| | ||  | |||||  | ||   
-----------------gttagttaatcctctgactggtctagctgctatttagttgc--atccaacatcctaacatgcttctgttc-------caacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
---------------------------------aatttcattagtgtgcaatcactatctctagagatctatagaaattttat----ctgaacac------ggactttggataccattgtgtttcc---------------ttctgtggagt--ctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                                 | ||   ||| |||     || |   |||| |   || |  | || ||      ||||  ||       |  ||  | |    |||  || ||               || ||| || |  || |||||||||||||||| ||||| ||||||||||| || || |||||||| ||||| ||  | || ||||| || || || || || || ||||| || ||   
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
---------------------------------aatttcattagtgtgcaatcactatctctagagatctatagaaatttt-----atctgaacacggac-----tttggataccattgtgtttcc---------------ttctgtggagt--ctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                                   |||  ||| | |  || || |   |||| |   || |  | || ||     |   | | | ||       ||  | |    |||  || ||               || ||| || |  || |||||||||||||||| ||||| ||||||||||| || || |||||||| ||||| ||  | || ||||| ||||| || || || || ||||| || ||   
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------aatttcattagtgtgcaatcactatctctagag---atctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                                                ||||| || ||||||  | | |  |    |||   |  |    |   || || | |    ||  |        |||  | ||  | |   |      |||||||||||||||||| || || || |||||||| || || |||||||| ||||| ||  | || ||||| ||||| ||  | || || ||||| || ||   
gtcagaattcagattatgaatcccaatcttgacaatgctctagtgtctatttcttt-gtgtgccttgagttgcgtgggagggtagttgctcaggattgatgttatggtggtttcctatggacataatattcacattaatttg--ttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4
---aatttca-ttagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
    ||  ||  |  |||     || |||||         |  || |  |||      | |  |  ||||  |    || | ||    | |         ||||| || |||||||||||||| ||||||||||| || ||  |||| |||||||||||  | || ||||| ||||| ||  | || || |||||| | ||   
gttgataccagctgatgtttttccaatatctt-----gcatcaaggagcttttctaataaaatgtttttgagtg--gttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA

upper sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------aatttcattagtgtgcaatcactatctctagagatctatagaaatttta--tctgaaca--cggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC
                     | |  ||    |    |   |   |     ||  | | | |  ||||  ||||||    |  ||| ||      ||| | | |  || | |     | ||||||||||| ||||| || |||||||||||||| || || |||||||| || || ||  | || |||||||| || || || || || || ||| | ||   
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA

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|162202022|gb|FC377228.1|FC377228
EST:     TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCG                         AGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT
genomic: TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT
EST: gi|162155347|gb|FC331246.1|FC331246
EST:     TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCG                         AGAAGGATTGGGAAGACATTAAATTTGGAGTAGAANATAAAGTTGATTTCT
genomic: TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT
EST: gi|162158981|gb|FC334828.1|FC334828
EST:     TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCG                         AGAAGGATTGGGAAGACATTAAATTTTGGAGTAGAAAATAAAGTTGGATTT
genomic: TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTT-GGAGTAGAAAATAAAGTTG-ATTT
EST: gi|162173132|gb|FC348705.1|FC348705
EST:     TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCG                         AGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT
genomic: TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT
EST: gi|100369821|gb|BY967400.1|BY967400
EST:     TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCG                         AGAAGGATTGGGAAGACATTTAATTTGGAGTAGAAAATAAAGTTGATTTCT
genomic: TCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCT

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: 31 (upstream exon), 34 (downstream exon)
Score: 6

CACGAGGAAGTGTACTGTGAAGTGGTGGATGGGGGTGAATTGAAGTCCCGTCGTCACCTCAACGTGCGCGGAAAGAGTGCCACTCTACCCTCCATTACCGgtacgacagt ... gagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - ctgaaca