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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT

Basic information

species Physcomitrella patens
transcript PP1S45_150V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g37210.1 (Oryza sativa), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
    |||  | | | |     | |  || |   | |   |||  | | || |||   | |   | |||| ||   || |  |          || | ||     ||| |    |   ||| ||| ||| ||      ||||||||||  | | || || |||||||| ||  || |||||||||||||||| ||||||||||||||||| ||||| |||||    ||||||||  ||   ||
----gtgagcgcgcgcgt-cagctttgc-tctgccgccattgatgagcatgcacaaagcta--gcttagattagcttatctt----------atgaatggtaactgata----tatccagcttctttgtttg-----tgcagGGCTCTCGAGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGTGGTCGCTTCTCCTTCGAGGAGGAGGAGGCCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g38740.1 (Oryza sativa), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctct--cctccttgataagtgtagcttgaaa-gtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
||||| |     |  | ||   |      | | |      || | |   ||    |  | || | |       ||   | |||    ||   |  |   || |   |||   | | ||        || ||   |     ||||||||| ||||| || || |||||||| ||| |  ||||||||||||||||  |||||||||||||| | ||    |||   | | ||||||| ||||  ||
gtaagcgccgcttatctagcttaaatttcttctcaacctctgcaatcc-tagctgcaatgttcggtcgaggcgatcgatcctcgaggctggctactctctgaactctgatctgaggtgcatgcaaaccgtgacaatcgtgtgcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGACTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGAGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g37970.1 (Oryza sativa), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                                       | | |  | |  || |       || || ||   ||||     ||  |   ||| |  |   |||         |||||| |   |    ||  ||   |||||  |  |  | ||||| ||||||||  |  || |||||||||||||||| ||||||||||||||| | ||    ||||| ||||||||||| ||||  ||
---------------------------------------tcgaaaagcactcatttgcacaatgatt-gtagaatttaacacctgatatctga-atcttctgctgatctagcctgatcaatgaacacc-ttgtgattcgcagGTTTGAACAGGTGTGGCAAGAGCTGCAGGCTGCGGTGGACGAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCTCCCAGGAGGAGGAGCAGACCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                                     | || | ||| ||         |     ||| |   |     |        || |     |  | || || |    |  ||  ||| |   ||| |   ||||||||||  | || || || |||||||| ||  || ||||||||||||||||  |||||||||||||||| || |  ||| |    |||||| |  ||   ||
----------------------------------ctctcttttcgtgcatgagaagtactcggtattattcacaggagctgagagactctagtccgttccatctggataacact--tcgttttgc---gttgc---atgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 1
gtaagt--ggtca-ctcacaagtggatgagcgtgcactgttgt-tgtagtgtatacactccgtttttgttta-gttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
||| ||  | ||  |||    | |   || |  |  | |  |  |   | |       |||  |  || ||  ||||  |||||| | | |   ||  |   ||  ||  ||      ||  |    ||  ||| | ||   |||||||||  | || || || |||||||| ||  || ||||||||||||||||  |||||||||||||||| || |  ||| | | ||||||| || ||   ||
gtacgtacgttcgtctcttttgcgatcgatctggggccgccgcgtcgcgcgcgcgtggtccagtagtgcttccgtttcgttttttttgtgcggttt--tcgctgaggc--gaggcgcgtgtgcgcgatcgatgggtgcg---tgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTGCGGCCGGACATCAAGCGCGGGCCTTTCACCCCGGAGGAGCACAAGTCCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G111117_T01 (Zea mays), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                                                      |  || |      |  |  ||| | |  |  || |   || |  | ||||||  ||            ||    |  ||  | ||||||  | ||| | ||||| ||||||||  | ||||||||||| |||||||| ||||||||||||||| | ||    |||     | | || || ||||  ||
-----------------------------------------------------gtgagtatggacagacctgaattctctaccatcttccaaatgaacgaagcttgtgaga-----------tctcgagcaacatactgcagGCTTGCAGAGGTGTGGGAAGAGCTGCAGGTTGAGGTGGACAAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCAGCTTGCAAGAAGAACAGACCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacact--------ccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttcc-ttggttacgaaat-gcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                                           ||   ||| |||| |  |  |       | |  ||  |  |  |     |         || |     |   | | |  |  ||||| |     |   | |   |        || |     |    || || |   || | | ||||||||  | || || || |||||||| ||| || ||||||||||||||||  |||||||||||||||| || |  ||| ||   |||||| |  ||   ||
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgc--gcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G032655_T01 (Zea mays), 3'ss of exon 1
gtaagtggtcactcacaagtggatgagcgtgcactgttgtt-gtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
    |||  |   |   || |    || ||      | ||| |||      | | |||       ||  | |    | |||   |    || | |     | |      | ||  |||  |      ||||        |||||||| ||||| || || |||||||| ||  |  ||||||||||||||||  |||||||||||||||| ||    |||   | | ||||||| ||||  ||
----gtgagcttgctatagcgagctagtgtagttactagttagtaacaatcaaagtccagcagcattcggctacgctgtttggtttgcgctggctcctccttgacatgca-tgcggatatggccgtgtggt-----gtggcagGGCTGCAGCGGTGCGGCAAGAGCTGCCGCCTCCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGGGGCAAGTTCAGCCTGCAGGAGGAGCAGACCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G111045_T01 (Zea mays), 3'ss of exon 1
---------------gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgta--tacact---ccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtg--------ttgatcagtttcct---tggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                | | | ||| ||       |      |   |   || ||  |||  ||  |   |    || ||  |||     |     |   ||    | |     || |    |     ||||        ||  ||  ||||     |||  | |  ||||||||||  | || || || |||||||| ||| || ||||||| ||||||||  |||||||||||||||| || |  ||| ||   ||||||||  ||   ||
gtcagaattcctctctttattagtcccttctcttcgcggtttccaccgtcgtcgtcttagcttagttctgcccgaccattggtgtcgcactcgcactggcctaaaatgccgaccaaattcctcgccggagtgaacgatgcttactctatttctgggatggcaatggcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACCAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACAGCCGAGGAGGAGAAGTCCAT

upper sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G166337_T01 (Zea mays), 3'ss of exon 2
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagct-tgaaagtgttgatcagtttccttg-gttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                                            |||      |  | |  | |    | |  |  |      | | | |  |||    || |  ||      | ||||    | ||   || | |    |||||||||   || || || |||||||| ||  || ||||||| |||||||| ||||||||||||||||| || || |||||    ||||||||  ||   ||
--------------------------------------------gtgagcgagcgacctgctggccccgatcgacgtcgatcatgcgcatatatacacatatccatgctcacctcgatcgtccttctcatgtcatg----gcagGGCTCGCACGGTGCGGGAAGAGCTGCCGGCTGCGGTGGACTAACTACCTGAGGCCGGACATCAAGCGCGGCCGCTTCTCCTTCGAGGAGGAGGAGGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT
                       tgttgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacactccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttccttggttacgaaatgcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG