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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG

Basic information

species Physcomitrella patens
transcript PP1S68_114V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
--------ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgc--agGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
               |     |  |       |   |        || ||            | |      |   | |   |   |      |  | ||| | |||  ||| |||||||||||| |    ||||||||||||| ||||||||| || ||| || | ||| |   ||| ||||| |||||||||||||||||||  || | 
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatc-ttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
       |  ||   |  |  ||   | |    ||| | | |  | ||         ||   ||||  |  |||   | |||  |  ||  |||    |||| |||||||||||| |    ||||||||| ||| ||||||||| |||||| |||| ||| |   ||| ||||| |||||||||||||||||||  || | 
-------gtgagctctcgtatttaccgct---gatggcctctccgattcgcatgcgtgggtcttac-cgtgtgtc-gtatcattttgtcgctgtggcacagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 1
ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacg-gtggttacatgcat-gtttatgtcaaatgatct---tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
                         |||    ||||   | | |  | |  |   | | |    |    || | || | | ||  ||  |||    ||   ||||| |||||||||||| |    || |||||||||| ||||||||| || ||| |||| ||| |   ||| ||||| |||||||||||||||||||  ||   
------------------------gtgagca-aatgttctgtggtctctccgtgcaggcgaacctttgcgcgtcgtctctctctgatagtctgttcgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 1
ggttgt-tggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaa---tgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
    || || |  |   | | ||   |   |   ||| | |||  | | |||   |   |    || | |    || | |   ||   |||| ||    | |||| |||||||| ||| |    ||||||||||||||||||||||| |||||| || | || ||   | | ||  | || ||||||||  | ||||  ||   
----gtatgtttctcactattatctctctctcagatgtcgtttctg-tattgttcattagattctagaagttaattaaggatgaaatgtgatttttgattacagGTGCGTACAAATACGTGTCGGAGCTATGGAGGAAGAAGCAGTCGGATGTGATGAGGTTTCTTCAGAGGGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------ggttgttgg------tagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttc-tgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
                                            | || || |      |    || |  ||||||  ||  |||||  |||  |   ||  | | | ||  || ||  | |  ||| |   |||||| |  ||  |  ||| |||||||||||  |    ||||||||||||||||| ||||| |||||| || |||||||   | | ||  | |||||||||||||| ||||  ||   
gtaaatccttcttctccatcccttcttctagatcaaatcctctcgtttcttagatcgattcagcttctccattgtttgttcaaatgatgtttctg---ttacgtatctgttattgcaaac-tactta-gcttaatgatttgattgatatagGTGCGTACAAGTATGTATCTGAGCTATGGAGGAAGAAACAGTCCGATGTGATGAGATTCCTCCAGAGGGTTAGGTGCTGGGAGTACAGACAGCAACCTTC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP06755 (Chlamydomonas reinhardtii), 3'ss of exon 1
ggttgttggtagtgtttttgattgttgattggaat-gacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG-----------
           |||   | | |    |  |   |    ||| |   |     ||   | |   ||   || |  |    | |   |     | | ||     | || |   ||||||||| ||||| ||| | |||||||||   |||||||| || |||||  |||||||||| |||||||||||| | ||| | ||  |           
-----------gtgcgatagctcaaagcctcataccagcatctgcagccgccgg---ccgacattctctgaacttacgcgactggtcgctctttccttggaccccgca---gTACATTGAGGAGCTGTGGCGCAAGAAGCAGAGCGATGTGCTCCGCTTCCTGCTGCGTGTGCGCTGCTGGGAGTACCGCCAGATGCCCAGCTGCGTGCGCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 1
ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
                  | |    || | |  || |   | |||   | |     |  |  |  |  |  || |    |    |   ||   ||| |||| || ||||||||||| || ||||||||| |||||||||| || |||||| |||| |||||  |||| || || |||||||||||  | |||||||| ||
-----------------gtaagcactgctcg--atca-gctcaggcgctcg-----catttctctcgcggctgatcgcattcctt--cctctctctccagGTGCCTACAAGTACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 1
ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
                  | |  |||| | |  || |   | |||   | |     |  |  |  |  |  || |    |    |   ||   ||| |||| || ||||| ||||| || ||||||||| |||||||||| || |||||| |||| |||||  |||| || || |||||||||||  | |||||||| ||
-----------------gtaagcgttgctcg--atca-gctcaggcgctcg-----catttctctcgcggctgatcgcattcctt--cctctctctccagGTGCCTACAAATACATCGAGGAGCTATGGCGGAAGAAGCAATCCGATGTGATGCGCTTCCTGATGCGCGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGG

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|18327613|gb|BJ159616.1|BJ159616
EST:     GCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|18355874|gb|BJ187933.1|BJ187933
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|67704760|gb|BJ964993.1|BJ964993
EST:     CTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: CTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|162203238|gb|FC379335.1|FC379335
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|162260329|gb|FC435632.1|FC435632
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|18349166|gb|BJ181215.1|BJ181215
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|37824878|gb|BJ582944.1|BJ582944
EST:     ATCCCTCAACCATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTG
genomic: ATCCCTCAA-CATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTG
EST: gi|18353919|gb|BJ185974.1|BJ185974
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|67719044|gb|BJ969303.1|BJ969303
EST:     CTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: CTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|162260330|gb|FC435633.1|FC435633
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
EST: gi|18345767|gb|BJ177810.1|BJ177810
EST:     GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGG                         GCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC
genomic: GCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGC

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), 33 (downstream exon)
Score: 33

TGACGAAGGCGGCTCTGTGCTCTTTGATCCAAGTGCTCTGCTGAATTGCTGCTCTGTTTGCGCGATTGCCCCTGCGCGTTGGCGCCATCCCTCAACATGGgttcgagcta ... tgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG
                                          tcttgttct  CT-rich tract
                         atgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgcagGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgc