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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG

Basic information

species Physcomitrella patens
transcript PP1S28_15V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
-----------cttcgata--gctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
           || |||    ||  |  | || |  | | |  ||  |||           |   |     ||     | | |   | |  |   | |||||| | ||   ||| |||||||| ||| |   |||||||||| ||| ||||||||| || ||| || | ||| |||  || ||||| |||||||||||||||||||  || | 
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctc---catctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatg-gggtttcg----gggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
               ||  |    ||   ||   | || | |  |   ||| | |  |  | |||| |      | ||| |||   |||||    ||  |   ||| |||||||| ||| |   |||||||||||||| |||||||||||||||| |||| ||| |||  || |||||||||||||||||||||||||  || | 
--------------gtgagctctcgt-atttaccgctgatggcctctccgattcgcatgcgtgggtcttaccgtgtgtcgtatcattttgtcgctgtg-gcacagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaat-tgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
               ||  |   ||||   |  | |  |  |||  ||||||  | ||   |  || ||       |  |  | ||||     | |   |||||||||||| ||| |   ||| |||||| ||| ||||||||| || ||| |||| ||| |||  || |||||||||||||||||||||||||  ||   
--------------gtgagcaaatgttctgtggtctc-tccgtgcaggcgaacctttgcgcgtcgtctct---ctctgatagtctgttcg---tcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttag--tgttggcgaattg--tgtatggggtttcggggtcttatttatttgttttggtt--tgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
                      |||     ||  | |   ||   ||   ||| | |  || ||||| |||   ||| |  |  ||   || | | |   |   |||||||||||| ||  |   |||| ||||| ||| |||||| ||||| ||| |||| ||| |||  || |||||||||||||||||||||||||  || | 
----------------------gtgagttctcg-gctacaaggccgtctccgattcgcatgcatgggtttttacggtatgttgcatcgtttctcgctgtggcgcagGGGCGTACAAGTATGTCTCGGAGTTATGGAGGAGGAAGCAATCCGACGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
cttcgatagctac--gttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttat-ttgttttggtttgtt-tagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
  |  ||||||    |||   | | ||    |   ||| ||   |||    ||| |||   ||    |     || || ||||| ||| | || || |   |||| || ||||| ||  ||   ||||||||||| ||||||||||| |||||  |||| |||||||  || ||| | ||||||||||| |||||||  ||   
-atatatagcttttggttattctgatggaattatgtgtggtacctgtgttggaagtgtaattga---taaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttca-tgttgttag-tgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
   |  |   | | | |||    || |  |  | ||   ||||   |||     ||  | ||| |        |  |  |||||| |  |  |||    |||| || ||||| ||  ||  |||||||||||| ||||||||||| |||||  || |||||||||  || ||| | |||||||||||| | ||||  ||   
--gcctttctttcatagcatttttgctattcaagtgaaattaggcattgtttgttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G15230.1 (Glycine max), 3'ss of exon 1
cttcgatagctac--gttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
    |||  |||   |||   | |||   ||||  | |  | ||  ||   |   | | ||  |   || ||  |  | | | || ||||  |||    |||| || ||||| ||  ||  |||||||||||| ||||||||||| |||||  || |||||||||  || ||| | |||||||||||  | ||||  ||   
tgctgatttctattagttatgctggttgagctttctatcat-agcatttttgttat-tctagtgaaattaggcattatttgtgttggtttatgttgcaatagGTGCCTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTATCGCCAGCAACCTTC

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP06755 (Chlamydomonas reinhardtii), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG-----------
               |||    |  |     | |  |   ||  |  ||       |   |   ||    |  ||||      || |     ||   | ||  |   ||  |||||||||||||| ||||| |||||||||  ||||||| | || ||| |||| ||||||||||||||||||||| | ||| | ||| |           
--------------gtgcgatagc-tcaaagcctcataccagcatctgcagccgccggccgacattctctgaacttacgcgactggtcgctctttccttggaccccgcag-

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
                      |   ||||  ||      ||    ||||  | |  | |    | ||| ||        |||  ||    | | |  ||| || ||||| ||||| ||||||||||||||||||||||| ||||||||| |||| ||| || | || || ||||||||||||||  | ||||| |||||
------------------gtaagcactgctcgat-----cagctcaggcgc-tcgcatttc---tctcgcggctgatcgcattccttcctctctctccagGTGCCTACAAGTACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

upper sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 1
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
                      | ||||||  ||      ||    ||||  | |  | |    | ||| ||        |||  ||    | | |  ||| || ||||||||||| ||||||||||||||||||||||| ||||||||| |||| ||| || | || || ||||||||||||||  | ||||| |||||
------------------gtaagcgttgctcgat-----cagctcaggcgc-tcgcatttc---tctcgcggctgatcgcattccttcctctctctccagGTGCCTACAAATACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

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|162231340|gb|FC406763.1|FC406763
EST:     GTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|18359307|gb|BJ191367.1|BJ191367
EST:     GCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|18330092|gb|BJ162098.1|BJ162098
EST:     GCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|162264017|gb|FC439247.1|FC439247
EST:     CTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: CTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|18327594|gb|BJ159597.1|BJ159597
EST:     GCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|162264016|gb|FC439246.1|FC439246
EST:     CTTGCGTNGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: CTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|37852702|gb|BJ610710.1|BJ610710
EST:     GTCGCGCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GTCGCGCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|18359292|gb|BJ191352.1|BJ191352
EST:     GTCGCGCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GTCGCGCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|162277019|gb|FC453741.1|FC453741
EST:     CTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: CTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|37852717|gb|BJ610725.1|BJ610725
EST:     GCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: GCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
EST: gi|19789799|gb|BQ041520.1|BQ041520
EST:     TTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGG                         GGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT
genomic: TTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGT

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: 33 (upstream exon), 35 (downstream exon)
Score: 14

AGGTCGCGCTTGCGTTGTCGACTCCGCGACTCAGAAAAATTCCTCGTCATGGgtacttgcac ... gtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG
                                              tttgttt  CT-rich tract
                           tcttatttatttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcgatagctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - tgcttca