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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtacttttggtttgattttaaacaggaggagatgtccaattatttgggttcctgtaaaatttgaatcgaggttgacctgtttataatctat...

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 10
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaag-ccgtgtacttttggtttgattttaaacaggaggagatgtccaattatttgggttcctgtaaaatttgaatcga---ggttgacctgtttataatctat---------------------
|||| ||     |||||||||||||||| || ||||| ||  | ||  |||| |||||||| ||| |||| |||||||||||||| |||||||||||||||| || || | |  |  ||   |  |||| |        |    |  | ||| ||       | ||  |     |||     | |||||    |||| || | |                     
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCACACTCGGTTCAAATTATTTTGCCTCAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctag

upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 10
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtactt---ttggtttgattttaaa-caggaggagatgtccaattatttgggttcctgtaaa-atttgaatcgaggttgacctgtttataatctat------
|||| ||     |||||||||||||||| || ||||| ||| | ||  |||| |||||||| ||| |||| ||||| |||||||| || |||||||||||||||| | |   ||    |||   |  ||| |   || |  ||    |   ||      | |  || |         |||   | |    ||||   || ||| |      
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGAAACAACTTGGACGTAGATCAGACATgtaaggccttctctcatgttgaactagtttcatctcatgttgaacacttttatcgaacagatcactatgcttgacacaattatgatatttctgtcggtattctctttttag

upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G318942_T01 (Zea mays), 5'ss of exon 7
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtacttttggtttgat--tttaaacaggaggagatgtccaattatttgggttcctgtaaaatttga-atcgaggttgacctgtttataatctat--------------
|||| ||     |||||||||||||||| || ||||| ||  | ||  |||| |||||||| ||| ||||  ||||||||||||| |||||||||||||||| || | |   ||  || |   ||  |||  |    |  | ||| | |  | |      |  | | |||      |    | |||||    |||| || | |              
GTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAACGAGTCCCACTCGGTTCAAATTATTTTGCCTTAGAAGCAACTTGGACGCAGATCAGACATgtgaggccttctctcatgctgaaatagttttcatttcatta-atgactagatttaaacacttttatcaaacagatcactatgcttgacacagttatgatatttctatctctttctag

upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 9
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagc----cgtgtacttttggtttgattt--taaacaggaggagatgtccaattatttgggttcctgtaaaatttgaatcgaggttgacctgtttataatc-tat---
| || ||     |||||||||| || || ||||||||   | | ||| |||| || || |||||  | ||||||||||||||||||||||||||||||||| |||     | | ||   |      |||||    |  |   |    |||   |   |     ||| |||     |    | |      | ||   | ||  | ||    
GGGCAATTGCTATCATGAGCCATCCCATCCCAAATACTGCTGAATCTCACTCAGTACAGATCATATTACCACAGAAGCAACTTGGCCGCAGATCAGACATgcaagtatttcttatatcatctcccagatttatccattatttgcttgtgtttcaccttcacatttcttgtgtttctaatgtgggaagcaatcttcatgtatgcataccag

upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA08G07250.1 (Glycine max), 5'ss of exon 10
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaag----ccgtgtacttttggtttgattttaaacaggaggagatgtccaattatttgggttcctgtaaa-atttgaatcgaggttgacctgtttataatctat
|||| || ||  | ||||| || || |||||| | |||||  | ||| |||| |  ||| ||||||||||||||||||| ||||| ||||  ||||| |||||||    |  ||  ||  ||   || ||| | |    |  | |||  ||   |         |  |||  |  || |   |||   |    |||         
GTGCAATATGTATTATGAGTCATCCTATTCCAGACACCAAAGACTCTCACTCAGCGCAAGTCATTCTGCCACAGAAGCAGCTTGGTCGCAAGTCAGATATgtaagttttctttgatctactgcgatgctttcacattttactaaatgcacatgaaaagaacaaaccataagcaaatgcacaaaggaacagacatttcctg-----

upper sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G09550.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtacttttggtttgattttaa--acaggaggagatgtccaattatttgggttcctgtaaaatttgaatcgaggttgacctgtttataatctat---------
| ||  | ||  | |||||||| || |||||| | || ||| || || |||| |||||||||||||| || ||||||||||| || |||| ||||||||||||||     || |   |     |||  ||  |||| |  |    |  |  |  || | |||   |   |      |  || |  | || || |   | |           
GAGCGGTGTGTATAATGAGCCATCCTATTCCAGACACAAATGATGCTCACTCGGTTCAAATCATTCTTCCTCAGAAGCAACTCGGTCGCAAATCAGACATgtaagat-catagtcaagaacacattcaaattacagaaacatgcatgtatctgatttgtttctactttgaaacagttgaagataaatctcttgagtttttggattttgtag

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|67694426|gb|BJ954659.1|BJ954659
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|37851885|gb|BJ609893.1|BJ609893
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|208363930|gb|DC947202.1|DC947202
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|18333101|gb|BJ165115.1|BJ165115
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|162196486|gb|FC375439.1|FC375439
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|161970273|gb|EE296246.1|EE296246
EST:     TCCGTNCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGT
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGT
EST: gi|162180983|gb|FC358637.1|FC358637
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|37827350|gb|BJ585362.1|BJ585362
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAATTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|37844517|gb|BJ602525.1|BJ602525
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|162229880|gb|FC404333.1|FC404333
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|37836338|gb|BJ594346.1|BJ594346
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|162166682|gb|FC342651.1|FC342651
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|208374624|gb|DC948624.1|DC948624
EST:     AATCATTNTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: AATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
EST: gi|18341638|gb|BJ173673.1|BJ173673
EST:     TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACAT                         GTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA
genomic: TCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTA

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), 35 (downstream exon)
Score: 17

GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtg ... ttgctggcagGTATGTGTTCTGTTGCTCTCACTCTCACAATATAGCTGCAAAAGACAAGTACATCGCATTTGTTTCAGCAGAAGTGGAGACGGACACTCCGGAAGCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGAAGCAACTTGGCCGCAGATCAGACATgtaagccgtgtacttttggtttgattttaaacaggaggagatgtccaattatttgggttcctgtaaaatttgaatcgaggttgacctgtttataatctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA