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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttggatatgttgcaggagctcctgcatttatgagttgtagaatagttaacgatgatcatcagtgtgacgttgtccttttattctcttttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA

Basic information

species Physcomitrella patens
transcript PP1S433_16V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
tagttggatatgttgcaggagctcctgcatttatgagttgtagaatag--ttaacgatgatcatcagtgtgacgttgtcct--tttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA
    | |   ||||||   |   | |  |   |||  |||| |  |    ||   | |   |||  ||  | |    |  |   | || |  |  | |  | |||||||||||| | ||||| || ||||| ||||| || || |||||  | ||||| || || ||| | || ||||| ||||| ||||||||||||||||| |
----taggcgtgttgcttaatgacata-acgcatggtttgtggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA

upper sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
-tagttggatatgttg-caggagctcctgcatttatgagttgtagaatagttaacgatgatcatcagtgtgacgttgtccttttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA
 |  ||   |||| |  | | | |   |  |        || | || ||    | ||| || ||  |  | |      | |   |||   || | |||| |||||||||||| | ||||| || ||||| ||||| |||||||| ||||| ||||| || || ||| | ||||| ||  |||| ||||||||||| ||||| |
tttctttcttatgataactgaatcaagtttaagccccccttttggattaac--atgat-attattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA

upper sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
tagttggatatgttgcaggagctcctgcatttatgagttgtagaatagttaacg-atgatcatcagtgtgacgttgtccttttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA
   |   || | ||     | ||    ||  | | ||           |||||     || ||  | || |      | |   |||   || | |||| |||||||||||| | ||||| || ||||| ||||| |||||||| ||||| ||||| || || ||| | ||||| ||  |||| ||||||||||| ||||| |
--atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA

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|208363722|gb|DC954693.1|DC954693
EST:     CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAAC                         GTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
genomic: CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
EST: gi|208350251|gb|DC925727.1|DC925727
EST:     CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAAC                         GTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGC
genomic: CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
EST: gi|37832759|gb|BJ590771.1|BJ590771
EST:     CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAAC                         GTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
genomic: CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
EST: gi|208394845|gb|DC915638.1|DC915638
EST:     CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAAC                         GTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
genomic: CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
EST: gi|37823243|gb|BJ581309.1|BJ581309
EST:     CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAAC                         GTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT
genomic: CTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGT

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: 22 (upstream exon), 20 (downstream exon)
Score: 2

ATTCTGTAGGTAAAGATGGGTCTGCTACCAATCGAGAGGAGGCAGATGCTCGTTCAGTTTTTGTCGGCAACgtaatcactt ... ttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttaacgatgatcatcagtgtgacgttgtccttttattctcttttcttttcagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA
 agttaac  putative branch site (score: 2)
                         cgttgtccttttattc  putative PPT
                                 ttttattctctttt  TA-rich tract