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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA

Basic information

species Physcomitrella patens
transcript PP1S4_277V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                                    ||  ||   |    | |   |||| | |    |||||||  | | | |   ||   | || | || | | ||| |               ||||||||||| || ||||  |||||| |||| |||||||| ||| | || || || ||||||||||||||||| || |||||||||||||| ||||| || || |
------------------------------------gtgcttttctacaatgt---ttcaagttctgtcttattggaaacctgcttcgt---tcttatcaatagtttttgg---------------gtgcagATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 3
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaacc-ttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                            ||  |     | | |  |    || |  ||||  ||| |   | | ||| |       |  | |||| |  | |        |||| |||     ||| ||||||||||| || ||||  |||||| |||| |||||||| ||| |||| || || || |||||||||||||| || || |||||||| || ||||| || || |
----------------------------gtaaatatccattagtatcttttagaacttcagaatgcatgataactgataagcagttcctttggttctcatgaa-------tgttgtga-----atc-gtgcagATACACACATCTAAGATGACATTGGCAGATGATGTGAACCTGGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 3
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaacctt--attgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                                         | || | |   |   |  ||||| |   ||  ||| |||   |||  | ||   ||||||     | || |   | | | |  |  |||||||||||| || || | ||||||| | ||||||||||| |||||||| || || || |||||||| || || || || |||||||| ||||| || |||||||
----------------------------------------gtact-gtgacgtctgtaaatgataatatttgcattaacaatgttcttaataccctttgttc---ttattatagaaggttgtaaacttgtgcagATACACACATCGAAAATGACATTAGCTGATGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgt-taagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
      |    || ||   |  | ||||    || | |    | ||  ||| | || |   ||   | |||| | |  ||| | | | |  ||| | | | |        | ||||  | ||||| | |  ||||||||||||| || |||||| | ||||||||||||||||| || ||||| || ||||| |||||||| |||||||| ||||| || ||||| || || |
-----gtcggaatgactagt--tctgtga---aaacat----gtttttggttttcact---gacatatcttaat-attcctattctacttagttatatctcactaaaaggtcttatacttttgatattt--agATACATACTTCAAGGATGACATTAGCTGATGATGTCAACTTAGAAGAATTTGTTATGACTAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagac---tgttttgttatgatcttgatctg---tgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                                   |  ||   | | || | |   ||  || |||  ||   ||| | |||  |  | |   |||||| |  |   || ||    ||  || |  | ||   |  ||||||| || || || |||||| | |||||||||||||||||||| ||||| || ||||| || |||||||||||||| ||||| || || || || || |
----------------------------------acccaa---cataagatgt-tgtttctgctgattctatgtgatatcttaacatgcatactttgttcaatcatatgcttatacattctcatactttggaattaagATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
            ||  | |   ||||||   | |   |    | || |    | | |   || |  | |||| | |  | | | | | |   || | | |  |     |  ||||  |  |||  | |  ||||||| || || || |||||| | |||||||||||||| || || ||||| || |||||||||||||| |||||||| ||||| || ||||| || || |
-----------gtaggc-acattttgtgaaagcaagttttcagtttcac---tgcttcactgttatatcttaat-atgcttattctacttaattatatgactaaaaggtc-ttatacttctgaaattt--agATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTTGTTATGACCAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
             |||| | |||            ||   ||| ||  | |     |   ||||         ||| || ||   || |    | || | | |   | || | ||  | | ||  |    ||||||| || || || |||||| | |||||||||||||||||||| ||||| || ||||| || || |||||||| || ||||| || || || || || |
-------------aacccaagat-----------acgatgttgtttctgctgattctatgtgatatcttaacatgatactttgttcaatca--tatgcttaaa---tgttctcatactttggaatta---agATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGACGAATTCTCCGGAGCTGATATAAAGGCAATATGTA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
------gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
      |||   ||  ||| |   |       |  ||  |   || || | |  |   |    | |  |   |  | |   | ||||  |    |   | ||  ||||    | |  ||   || |  ||   ||||||||||||| || || |||||| ||||||||||||| |||||||| ||||| || ||||| |||||||| || ||||| ||||| || || || || ||||
gtacatgtgtgtttaagattatgcaaatgcaatattc--actatattttcatccgacttcttgtgacaactgaa-tcaccaa-acctggcttgattactattactaagcaaatctcattt--atttaaat---tgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

upper sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 4
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgt-taagactgttttgtt--atgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                                                                         ||||  | | |  | |   ||||||    |  ||||||     |  |  ||| |   ||||||| ||||| || ||||||||| |  |||| ||||| ||||| || || || |||||||| ||||||||||||||||| |||||||| || || || ||||
------------------------------------------------------------------------gtgacgtcgtgcttatt---ttttgtgcgcgtttgtttttcccaaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGATGAATTCTCTGGAGCTGACATCAAGGCAATGTGCA

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|162268182|gb|FC443860.1|FC443860
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|37841464|gb|BJ599472.1|BJ599472
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|22131707|gb|BQ826756.1|BQ826756
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|162258957|gb|FC435900.1|FC435900
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|37840238|gb|BJ598246.1|BJ598246
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|162216154|gb|FC392987.1|FC392987
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|37838576|gb|BJ596584.1|BJ596584
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|67578692|gb|BJ950859.1|BJ950859
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|15327439|gb|BI488180.1|BI488180
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|162224575|gb|FC400471.1|FC400471
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|37853193|gb|BJ611201.1|BJ611201
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|162243828|gb|FC423145.1|FC423145
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|18338331|gb|BJ170355.1|BJ170355
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|67724880|gb|BJ975139.1|BJ975139
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|37847407|gb|BJ605415.1|BJ605415
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
EST: gi|162171248|gb|FC346393.1|FC346393
EST:     AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAG                         ATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC
genomic: AGATCGAGTTTCCATTGCCTGATATTAAAACCAAGAGAAGAATTTTTCAGgtgatatttc ... atctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA
                                        tcttgat  putative branch site (score: 4)
               ttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatatttcgataacctatgatttgtggtcgaagcgtaattgcttgaggtatacattcatgatgaaccttattgacacctttcccagtaggttttgttaagactgttttgttatgatcttgatctgtgcagATACATACTTCTAGAATGACAATGGCTGATGATGTCAACTTGGAGGAATTCGTGATGACCAAGGATGAATTCTCTGGTGCTGACATTAAAGCTATCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG