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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
             | || || || | | |||    |||   |   | |   |||||     || ||    ||| ||| | |||||  | |   | |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||
-------------gtatgctagatc-tctgttacatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
             | || || || | | ||  |  |||   |   | |   |||||     || ||    ||| ||| | |||||  | |   | |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||
-------------gtatgctagatc-tctgctgcatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 5
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
             | || || || | | ||  |  |||   |   | |   |||||     || ||    ||| ||| | |||||    |   | |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||
-------------gtatgctagatc-tctgctgcatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtggttgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 2
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
             | || ||  | | | ||  |  |||   |   | |   |||||     || ||   |||| ||| | |||||  | |   | |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||| | || ||
-------------gtatgctacatc-tctgctgcatgagaggtggtatat-tttca----tagtttttcttgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 6
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
             | || || || | | ||  |  |||   |   | |   |||||     || ||    ||| ||| | |||||  | |  || |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||
-------------gtatgctagatc-tctgctgcatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtgattgtatgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
        ||||  | | ||      | ||           | | | |     |   |    |  |    |||  || | ||||| || ||| | |  |||||||||||||||||||| |||||||| || |||||||| || || || ||  ||||||| || ||
-------gtatactagttctctgctctgtgagagacagtacgttgtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg----gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
  ||||| |||   | | ||    | | |||    |   || |  | ||  |||||| ||    |||       || |     ||| | || |   |||| ||||| || |||||||||||||||||||| || ||||||||||| || || || |||||||| |||||
--tatatttattctacttct--gtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtg-cgtttcagtttcagattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
 ||||  ||   |      |   | |||  |      |||   | | |  |   | |   |        | |  ||| || |  |||| |   |||| ||||| || ||||||||||||||||| || || ||||||||||| || || ||||||||||| |||||
-atattaattctacttctgtcatgtgttattgcttgaaagttctgtttttcagctgatccttgagacactatctaatatgttaggaaaataatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
-tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtt-tgaaatttggtttgaaact-tcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
 ||  ||| | ||   |    | ||  |   | |  | || |  |   ||  | || |   | ||  |  | |  |||||    ||||||  | | ||| ||||| || ||||||||||||||||| || || ||||||||||| |||||||| ||||| || |||||
atagttatgtctagctactgct-agtatcattgg--tcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
----tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagat-tggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
    || ||  | ||     |  |       |  | |   ||     | | |    |  | ||  |||  |  | | | | ||    | |||| |    || ||||| || ||||||||||||||||| || || ||||||||||| || ||||| || || || |||||
ccagta-attcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacct----ttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
-tatata-tatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttca--gattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
 |   || ||  | ||| |   |    |         | |   |||     |   | | ||||    | |  | | | | ||    | |||| |    || ||||| || ||||||||||||||||| || || ||||||||||| || ||||| || || || |||||
atgcctagtaattcagattgtatttatgacctactcattagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacct----ttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
tatatatatataagaatccttgagcgtttgta-gagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttggtt--tga---aacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
                         ||| ||  || |  ||| ||||   | | |||  |||| ||       |   || |||  |||   ||  |  || ||||||| |||||||| |||||||||||||| ||||||||||| || || || || || ||||| |||||
-------------------------gttcgtgtgaatatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG-----------------------------------
  | | |  |      |   | |    | | | | ||       || |   |||  |  | |   || |   | ||    ||| |   |||   | |||||| || || |||||||||||||| || || |||||| | ||||| ||||| |||||||| |||||                                   
-gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgactta---tgatcatatatcct-tttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG

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|208360291|gb|DC943021.1|DC943021
EST:     ATCTGGCTTGTCCTGCTTCACCCATTTTCTACAAGTACAATGCCGTGAAG                         ACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAA
genomic: ATCTGGCTTGTCCTGCTTCACCCATTTTCTACAAGTACAATGCCGTGAAGgtaaactgtc ... cattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAA
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     CCTGCTTCACCCATTTTNTACNAGTACAATGCCGTGAAG                         ACCATCANGACAAATGTGATNGGTACGCTCAACATGCTNGGACTCGCTAAA
genomic: CCTGCTTCACCCATTTTCTACAAGTACAATGCCGTGAAGgtaaactgtc ... cattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAA

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: 30 (upstream exon), 35 (downstream exon)
Score: 8

ATGTGACAGAGACATTATTTGTTGAAGTAGACCAGATTTATCATCTGGCTTGTCCTGCTTCACCCATTTTCTACAAGTACAATGCCGTGAAGgtaaactgtc ... cattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcgtttcagtttcagattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG
                                          cttcatttt  CT-rich tract
                       tttgaaattt  TA-rich tract