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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttattgattgagatttttgctctgttcatgaatagttaggtatattgacacctctacacaaatgtag

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 4
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaaccttta--ttgattgagatttttgctctgttcatgaatagttaggtatattgacacctctacacaaatgtag
|||| || || || || ||||| |||||||| ||||| || ||||||||||| |||||||| || || |||||||| ||  | || |||||||| ||||||| ||     |  | || |      |  ||||    |  |  || | ||  |  |     | |||  ||||   |||  ||||  |  |                                                
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttg---ttcagattatttgggtgtt-----aaaaatgtttaatctgaaagagaaatcag------------------------------------------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g52840.1 (Oryza sativa), 5'ss of exon 4
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttatt----gattgagatttttgctc--tgttcatgaatagttaggtatattgacacctctacacaaatgtag-------
|||| || || || || ||||| |||||||| ||||| || ||||||||||| |||||||| || || |||||||| ||  | || |||||||| ||||||| ||     |  | || |      |  ||||    |  |  || | ||  |  |     | |||  |||| |     |  || ||   |||    ||    |||||  |  |   |  ||    ||||         | |       
AGAACTTCACCTCGGTGTCAGTGATGCAGGCGGTGGGATCCGTCATGACCAACAAGTACAGCGAGGGGTACCCCGGCGCGAGATACTACGGTGGAAACGAgtacggttgattgcgttctatcggttgcctttg---ttcagattatttgggtgtt-----aaaaatgtttaatctgaaagagaaatcagtgcctgatgggagtgaatgatgtgaatttctggtggctctgggttttccttgcgtgcag

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 4
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttattgattgagatttttgctctgttcatgaatagttaggtatattgacacctctacacaaatgtag
||||||| ||||| || ||||| ||||||||||||||||| ||||||||||| |||||||| || || ||||| || ||  | || ||||| || || |||| |     | |||  |    | ||  |||    | | |  |  ||    |  |   | || |     | | ||  || | |   |  ||||     |  |  |||  | | |     | |   | ||       
AGAATTTCACGTCGGTGTCAGTGATGCAGGCAGTGGGTTCCGTCATGACCAACAAGTACAGCGAGGGGTACCCTGGCGCAAGATACTACGGGGGAAATGAgtactgccctgctctatcggttgtcattctcgtgattgtttca-gtggaaacacgcgtgcaaattgagtgactgtctggg-tgaataatctgaattggggtttttat-tctgtgtgttcttggtcgcag------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EDO97448 (Chlamydomonas reinhardtii), 5'ss of exon 5
AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtttctcattttcctctctctctttaaaatataacttgtctgtattctttttcataaacctttattgattgagatttttgctctgttcatgaatagttag-gtatattgacacctctacacaaatgtag
                                |||||    ||||||||||| |||||||| || || |||||||| || ||||| ||||| |||||||||| | | |           |  || |  |        ||     ||| | |  || |||  |         | |     |     ||  |  |    |  | | | | | || |||      || | |   |    
-------------------------------GGTGGGCAGCGTCATGACCAACAAGTACAGCGAGGGCTACCCCGGCGCCCGCTACTACGGCGGCAACGAGTTCATTGACCAGGCAGAGCGCCTGTGCCAGgtgggaatctggggtccgcaggctgtttagtgggttgcggtgggcgaggggccgtggacgctgaggggcttgctggtggatcttgga---cctgcgcgggttc--

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|162179835|gb|FC355906.1|FC355906
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|162182305|gb|FC357176.1|FC357176
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18369273|gb|BJ201358.1|BJ201358
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|100385980|gb|BY951174.1|BY951174
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18365567|gb|BJ197644.1|BJ197644
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18362808|gb|BJ194880.1|BJ194880
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|208358811|gb|DC935197.1|DC935197
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|100428360|gb|BY977766.1|BY977766
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCNNNNNNNGAGCTCTCGCAGCTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAA-GAGCTCTCGCAGCTT
EST: gi|18361307|gb|BJ193373.1|BJ193373
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18374142|gb|BJ205720.1|BJ205720
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18369196|gb|BJ201281.1|BJ201281
EST:     AATAAGTACAGTGAANGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAA
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAA
EST: gi|208379665|gb|DC903720.1|DC903720
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|162155361|gb|FC331767.1|FC331767
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|18356126|gb|BJ188185.1|BJ188185
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTG
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTG
EST: gi|18366816|gb|BJ198896.1|BJ198896
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
EST: gi|100392460|gb|BY953374.1|BY953374
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCNNNNNNNGAGCTCTCGCAGCTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAA-GAGCTCTCGCAGCTT
EST: gi|18370401|gb|BJ202003.1|BJ202003
EST:     AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGA                         GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT
genomic: AATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTT

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: 32 (upstream exon), 8 (downstream exon)
Score: 2

AGAATTTTACGTCCGTATCAGTTATGCAGGCAGTGGGTTCAGTCATGACCAATAAGTACAGTGAAGGTTACCCCGGTGCTCGCTATTACGGTGGCAACGAgtgcgtagtt ... acaaatgtagGTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG




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