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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S13_236V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g36160.1 (Oryza sativa), 3'ss of exon 2
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                              | |  | |  |  ||||| |  |      || |   ||   | |||       || |||  | |  |  | || |||   ||     || ||||  |  || |   ||||||||||| || || ||||| ||||||||  | |||||||| ||||| || |||||| |  | ||||||||| | ||||||||||||
--------------------------------------------tattattgattgattcatgtgaaataggaactgcac--atgcaccgat-------gtatgtggagtcattgacatgtttga-atcactaat-gttttgttattctccacagAATGGTCTTGCCACTAAGGTAGAGAAGTCACGTAAGCAGATGAAGGAACGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 2
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttattttt-ttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggt-tatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                           | ||  | | |    |||| | | |||   |  ||||| | | ||        | |  | |||   ||||||    | | |  | ||        |||  ||   ||  | |||||||| || || |||||||| ||||||||  | |||||||| |||||| | |||||| |  | ||||||||| | ||||||||||||
-------------------------------------------ttttccatgat----gcatatcaatttaactcgtgaaacactatgaaagcccatgttttatgtat-tttgtc----tttctcatttt-----ctttttgctgccatacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G091383_T01 (Zea mays), 3'ss of exon 2
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                                       ||  |||||||  ||    |  | ||  | || |           ||| |  ||| |||  | |  ||  |    ||  |   ||  ||| | | ||||||| ||||| ||||||||||| ||||||||| | |||||||| |||||| | |||||| |  ||||||||||| | ||||||||||||
-----------------------------------------------------caaatccatgttacattgcaatgcagattttgtgattgaaacaacactgtctgtattggtcctgcttatttttgacaagagtgtgtt--tgggtttctgcagAACGGTCTTGCTACCAAGGTGGAGAAGTCGCGCAAGCAGATGAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGCGGTGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgtt-atttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtat-tgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                                             | || |   ||  | |||    |||  ||| ||| | |   |  |   ||||  |      |  |||  ||   ||  | |  |  |  |   ||||| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||
--------------------------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgtta-gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgtt-atttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtat-tgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG----
                                                             | || |   ||  | |||    |||  ||| ||| | |   |  |   ||||  |      |  |||  ||   ||  | |  |  |  |   ||||| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||    
--------------------------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgtta-gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G171426_T01 (Zea mays), 3'ss of exon 3
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaata-atttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgc-agAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                               | | |  | |   ||| |||||| |||||| | |  |  |  ||||||   ||        |  ||    ||| || | |||   |  |  ||   |  |  ||||| |||||||||| ||||| ||||| ||||||||  | ||||| || |||||||| |||||| |  | ||||||||| | ||||| ||||||
-----------------------------------------------gcatgcccgaa--atgatattttattgttgtattgtaagttttgattgacatga-------acctgatg-gatgttcactatactgcttttttgtgttctgttttgccagAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAGGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 3'ss of exon 3
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                          || || |||     | |  | |  ||||||  ||||| |  ||   ||      |   | |   |  || ||      | | | |||||      |||  || ||  | |||||||||  ||| |||||||||||||||||| |||||||| || |||||| | |||||  | || |||||| || | ||||| ||||||
------------------------------------------tttttaaaaaaatcacgtct-tccttttttctttgaact--ttaattgccctcctctctctaccccattttc-----ttcttgcattgaa-----tttgctgtttggtggcagAATGGATTGGATACCAAGGTCGAGAAGTCTAGGAAGCAAATGAAGGAGAGGAAGAATAGGTCCAAGAAGGTCCGAGGTGTAAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16004 (Selaginella moellendorffii), 3'ss of exon 3
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatt-tgctgattggtttggtgtgttcatttgtca-agatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                                                         ||     || || |  |||||   | || |  |||       | |||| | |    |||      ||||  |  |   || ||||| || || || ||||  |   | || |||||||||||| |||||||||| |||||| |  ||||||||||| | || |||||||||
-------------------------------------------------------------------------gtgagcttagttcttttgatt--ctcggcgccttcgcaaacaacagatttctcaccttg------gtttcgttttctgttccagAACGGACTTGCCACCAGAGAGCAAAAATCGAGGAAGCAGCTCAAGGAGCGGAAGAACAGAGCGAAGAAGATCCGCGGAGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07954 (Selaginella moellendorffii), 3'ss of exon 3
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatt-tgctgattggtttggtgtgttcatttgtca-agatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                                                         ||     || || |  |||||   | || |  |||    |  | |||| | |    |||      ||||  |  |   || ||||| || || || ||||  |   | || |||||||||||| |||||||||| |||||| |  ||||||||||| | || |||||||||
-------------------------------------------------------------------------gtgagcttagttcttttgatt--ctcggcgccttcgcgagcaacagatttctcaccttg------gtttcgttttccattccagAACGGACTTGCCACCAGAGAGCAAAAATCGAGGAAGCAGCTCAAGGAGCGGAAGAACAGAGCGAAGAAGATCCGCGGAGTGAAGAAG

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ29464 (Selaginella moellendorffii), 3'ss of exon 3
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatgg--ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                                                                   |  |   | ||   |  || |||  |            | | | | || | |  |    | |  |  ||||||||| || || || |||| ||   ||||||||||||||||| |||||||| | |||||| |  | ||||||||| | || |||||||||
----------------------------------------------------------------------------------gtgagtgaagtgagctcatg-gtttctcgacttgcgctctaactctggaagcttttccccttgcatcttttgcagAACGGACTTGCAACCAGGGAGCAGAAGTCGAGGAAGCAGCTCAAGGAGAGGAAGAACAGGGCCAAGAAGATCCGCGGAGTGAAGAAG

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|67722633|gb|BJ972892.1|BJ972892
EST:     CTCCATTGACTCTGCTTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: CTCCATTGACTCTGC-TAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|37822925|gb|BJ580991.1|BJ580991
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|37850086|gb|BJ608094.1|BJ608094
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|37825316|gb|BJ583382.1|BJ583382
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|37852779|gb|BJ610787.1|BJ610787
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|162218184|gb|FC394189.1|FC394189
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|162169907|gb|FC345847.1|FC345847
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|208387629|gb|DC953371.1|DC953371
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|67692745|gb|BJ952978.1|BJ952978
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|162218185|gb|FC394190.1|FC394190
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
EST: gi|208370058|gb|DC940365.1|DC940365
EST:     ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGG                         AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC
genomic: ACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGC

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: 32 (upstream exon), 35 (downstream exon)
Score: 19

CAGAACGCATTTCGGAGGTGGCAAGTCCACTGGATTTGGTCTCATCTACGACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattca ... ttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG
                                    gtttaat  putative branch site (score: 19)
                                     tttaatggttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG