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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttgcatcgatagtatcacggatgagacctgcacaagaaaccctttctgttttctgatggaggaggaatactgactgtccctggtttgtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT

Basic information

species Physcomitrella patens
transcript PP1S367_8V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S367_8V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 10
------------------------------------------tgacttgcatcgatagtatcacg-gatgagacctgcacaagaaaccctt--tctgttttctgatggaggaggaatactgactgtccctggtttgtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAAT-AAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT
                                          ||| | |    || | | |     | || |   ||   |   |    ||  || | |||   ||    |        ||  | ||    || | | ||  ||| | || ||| |||||||||||||||| |||||||| ||  |||||||||| |||| || |    ||  | | | |  |    || ||  ||    | | | 
gtcaggcatttttctttttgcttttccactgctctttttatttgagtagggatgaaaatctagtttggtgggggatgttgagttaggttttgatcggcttttgcatttttgccctgacatggttttcgtatgtat-taattgcagCTTGACCACAGGAAAAAGGACTACAAATTTGGGTTTGGTTTGACTGTGGGAGAATGAATAAACCGAACTGGAGCTGTGTTTTCATTGCTGTACCCAGCTT-

upper sequence: PP1S367_8V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ15593 (Selaginella moellendorffii), 3'ss of exon 10
tgacttgcatcgatagtatcacggatgagacctgcacaagaaaccctttctgttttctgatggaggaggaatactgactgtccctggtttgtgatgcc-agATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT
                                ||||       |  | ||  |  |    ||           || |||  || || |    | |||| |||| ||||||||||| || |||||||||||||| |||||  |||| || || || | |                                           
-----------------------------gtttgcatcgccgccattgtcaatacttccttg-----------ctaact-cccgtgctgctggctgcccagATTGATCACTGGAAGAAAGACTACAAGTTTGGTTTCGGGTTGACGGTTGGGGAGTGA-------------------------------------------

upper sequence: PP1S367_8V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ38844 (Selaginella moellendorffii), 3'ss of exon 10
tgacttgcatcgatagtatcacggatgagacctgcacaagaaaccctttctgttttc-tgatggaggaggaatactgactgtccctggtttgtgatgcc-agATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT
                                              |||   |   |   || |   |    | || |||  || || |    | |||| |||| |||||||||||||| |||||||||||||| |||||  |||| || || || | |                                           
---------------------------------------------gtttgcatcgccgccattgtcaatacttgctaact-cccgtgctgctggctgcccagATTGATCACTGGAAAAAAGACTACAAGTTTGGTTTCGGGTTGACGGTTGGGGAGTGA-------------------------------------------

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|162208677|gb|FC385074.1|FC385074
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTTTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|37846861|gb|BJ604869.1|BJ604869
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|67725480|gb|BJ975739.1|BJ975739
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|162224207|gb|FC399271.1|FC399271
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|208370718|gb|DC948255.1|DC948255
EST:     ATCCTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|208360525|gb|DC950071.1|DC950071
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|162209490|gb|FC386123.1|FC386123
EST:     TTCTTGAGGAGAGACTTAACCTGGGTGTCAATTTCTTGCTTTTTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|67699473|gb|BJ959706.1|BJ959706
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|162242295|gb|FC418872.1|FC418872
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|37821417|gb|BJ579483.1|BJ579483
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|162208676|gb|FC385073.1|FC385073
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTTTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|208353007|gb|DC926072.1|DC926072
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|67726076|gb|BJ976335.1|BJ976335
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|208348734|gb|DC926409.1|DC926409
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|208357443|gb|DC953767.1|DC953767
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
EST: gi|37823603|gb|BJ581669.1|BJ581669
EST:     ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAG                         ATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC
genomic: ATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGC

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: 14

TGCCGTTTGAGGGGAAGGTTGGACACAAATGGTTGTATCGCAGCTTATCTTGAGGAGAGACTTAACCTTGGTGTCAATTTCTTGCTTTCTGCGGAGgttagtgttc ... gtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgttttctgatggaggaggaatactgactgtccctggtttgtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT
                          tactgac  putative branch site (score: 14)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttgcatcgatagtatcacggatgagacctgcacaagaaaccctttctgttttctgatggaggaggaatactgactgtccctggtttgtgatgccagATCGATCACTGGAAAAAGGACTACAAGTTTGGGTTCGGCATGACTGTGGGCGAATAAGACTATGATGTAGGGTTAGGAAGGCACTGAGGTTATGATCATT

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