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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctgatcccctttatgaatcatcatgcaattattggtggagagtccggatgcctagcatatctcacagtagcggtgttcgaaaaaggaattaga...

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA12G06980.1 (Glycine max), 5'ss of exon 10
AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctgatcccctttatgaatcatcatgcaattattggtggagagtccggatgcctagcatatctcacagtagcggtgttcgaaaaaggaattaga---
 || ||  |  | || || || | |||||| ||||||||||| ||||||||||| |||||||| |||||| ||  |   |   ||| |   |     ||   ||||   | ||   | |   | |   |  |   | ||  |     | |        | ||||      
TGGTGAACCCTTAACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTTTGCTATGTCTCTGACATGgtatatattatacttgtttctcttttga-gtgttgttatc--ttga---ttcaagtactaggtgtgattgactatgatcatatatacgcttgaaatttattag

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 10
AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctgatcccctttatgaatcatcatgcaattattggtggagagtccggatgcctagcatatctcacagtagcggtgttcgaaaaaggaattaga
 || ||  |  |||| || || | |||||| ||||||||||| ||||| ||||| |||||||| |||||| ||      |   ||| | | |  | ||  | ||||   | ||   | |   | |   || |   | ||        |       |||   ||||| 
TGGTGAACCCTTGACTGTCCAAGTTCCAGGAACTCAAACTCGCAGTTTCTGCTATGTCTCTGACATGgtatatatgatacatgtttcttatttgtgattta-ttatc--ttga---ttcaagtactaggcgtgattgactaagattatacatttgaaatctattag-
















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|15728950|gb|BI741060.1|BI741060
EST:     CTCGGAGTTTTTGCTACGTCTCTGATATG                         GGAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: CTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|208390897|gb|DC945914.1|DC945914
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|37850860|gb|BJ608868.1|BJ608868
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|67692844|gb|BJ953077.1|BJ953077
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|67697660|gb|BJ957893.1|BJ957893
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|208385608|gb|DC948967.1|DC948967
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|37843082|gb|BJ601090.1|BJ601090
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|208370456|gb|DC952159.1|DC952159
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|37830721|gb|BJ588733.1|BJ588733
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
EST: gi|208371231|gb|DC956009.1|DC956009
EST:     TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATG                         GTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT
genomic: TGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAAT

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: 12 (upstream exon), 26 (downstream exon)
Score: 3

AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctg ... gtgcgtgcagGTAGATGGTTTGTACCGGCTTATGAATGGAGACCATACTGGGCCTATCAATATCGGCAACCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGGAGACGATGACGGTGCAGGCTCCAGGCACTCAAACTCGTAGTTTTTGCTACGTCTCTGATATGgtacatcctgatcccctttatgaatcatcatgcaattattggtggagagtccggatgcctagcatatctcacagtagcggtgttcgaaaaaggaattaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaggaa