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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatc-tgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
       |        ||| | |  ||||    ||        | |   || ||  |  |  |||||       | |   | | |     |     |  || ||||| |||| ||||| |||||||||||||||||| || |||||||| ||||| || ||||
-----gtaagagaaaagctattc--atttctgctagtttgttgaagcttaattatgtttttttttctccccaaaaacactcattgaagaaaaatgatacagTTTTGGGCAGCTTATCAGAGTTAATTGGGCATATGCTAGTGGGCAGAGGGAGGACACAACAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                       ||| | |   |    |          |||| |||  | ||||  | |||| || |   |       ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  |||
----------------------gtaagtgttgctctttagatttatgttaaattgatt-tcattttgtattctaattttaatt----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                       ||| | |   |   ||          |||| |||   | ||| | ||     |||   |       ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  |||
----------------------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaattctaatt-----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
              ||      ||||  ||  |     ||||   ||  |   |  |  |   |   || ||| |  |   |  |  ||    |    ||||||||||||||||| |||||||||||||| |||||||  || || || || |||||  || 
--------------gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagat-tataatattgg-atttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 4
--cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
        || ||||  |  ||||||   | ||||               |  || | | | |   | || ||  | |     |  |  |   | | |  || |||||||||||||||||||| |||||||| ||||| |  || ||||| || |||||  || 
gtaaggaacaattttcatagtttccttcctctcctctt------------cttatcgttcgaatgcttttgtttaggtt---ataatcgtcgagtt-tacagGTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagat-----agtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                                    | | | |   | |  ||||||     | | | || ||   ||  | |   |    ||| |  | || || ||||| ||||| ||||||||||||||||||||||| ||  | ||||||||||||||  |||
------------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
          |     |    | | |||||  ||    |||  |    ||  | |  | |  ||||| || || || |            |  | || || ||||| ||||||||||||||||||||||||||||| || || || || ||||| ||  |||
---------gtaagaagaacccttgatttttattt---atgtta----catgttgggatttgtttctgttgctcatttt----------gtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

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|208376147|gb|DC910999.1|DC910999
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGA
EST: gi|162258161|gb|FC433943.1|FC433943
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|208368756|gb|DC940051.1|DC940051
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|100450649|gb|CJ974369.1|CJ974369
EST:     GAC-ATATTTATGCTGCAGTAGCATTAACTACTCTAA-TGGCANANTAAT                         ATTTGGACAGCCTATCA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCA
EST: gi|162254430|gb|FC430656.1|FC430656
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|208391587|gb|DC933836.1|DC933836
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAA
EST: gi|162277159|gb|FC453381.1|FC453381
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|100409806|gb|BY956113.1|BY956113
EST:     ACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACNTA-T                         ATTTGGACAGCCTATCAAAGGTAATTGGGCATATGCAAGCGGGCAGAGAG
genomic: ACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGAC-TAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAG
EST: gi|162152881|gb|FC328975.1|FC328975
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|162261365|gb|FC437798.1|FC437798
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA

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), 31 (downstream exon)
Score: 7

TCATCATATGGATTTGTTGACTACTTGGACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                        ttctgat  putative branch site (score: 7)
     aatagatagtaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT