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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

Basic information

species Physcomitrella patens
transcript PP1S384_37V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttg---ggtcttctgtgaggtgcagtgagtcagggttaggt-ttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttc--agGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                         |  ||    |||||  |  |    ||   ||||     ||    |||  | |    | | |     |  | | ||     ||| |   ||   |||  |  | |  |   ||    |  | | ||    || || |||||||||||||||||||||||||| ||  |  | ||| || | ||| |    ||||| |||||
---------------------------------------------------------gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                                              ||| |  || | |  | | || |    |  | ||| | | |  | |  ||    |  | |  | ||| |    ||   | ||  |||         | |  |||||  ||||||||||||||||||||||| |||||  || | ||| |  |||                   
------------------------------------------------------------------------------atgctttgc-tggcctatgctatctattaaattgatttatgtattgcatta---atatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAAT-------------------

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                                              ||| |  || | |  | | || |    |  | ||| | | |  | |  ||    |  | |  | ||| |    ||   | ||  |||         | |  |||||  ||||||||||||||||||||||| |||||  || | ||| |  ||||  |    |||   || ||
------------------------------------------------------------------------------atgctttgc-tggcctatgctatctattaaattgatttatgtattgcatta---atatcatcattttatttgattttctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                           ||  ||   | | ||   | |  |    ||||  | ||   |      | |||  |  |  ||  |  ||      | |  | || |  |  |   ||  |  ||                ||||||||||| |||||||||||||||||||| ||  || | ||| || | ||| |   |||||| |||||
-----------------------------------------------------------gtacggagctcctcaatcctt--tcattgttgactttttctt----ctctgtgcatgcgttttgagcctgcttg--tgataatttgggtgtgtgtatttttctctaa--------------agGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgttt---cagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                           ||||   ||       |   | |    | ||  ||| |  |||  |   | | |||  |  |||  ||| |||   | | |   |    |||||      | |  ||  || |  ||| |    || |||||||||||||||||||| |||||||| ||  || | ||| || | ||  |  | ||||| |||||
-----------------------------------------------------------gtgtacaaagctcttccttttctgtaaccttttgtcat--gtggtggttaatcagtttgtatta--tttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtg-cagtgagtcagg--gttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgttt---cagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                                    | |  ||| | |  |   |  |    ||| ||| | |||   || | ||||   ||    ||| |||   | | |   |    |||||      | |  ||  || |  ||| |    || |||||||||||||||||||| |||||||| ||  || | ||| || | ||  |  | ||||| |||||
-------------------------------------------------------------------gtacaaagctcttccttttctgtaa-ccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                                                                             |  |||  | ||| |  ||||| |    |    ||       |||  | | |  |   |      | | | |  ||| |    | |     ||   |||    ||||||||||| ||||||||||||||||| || ||| |  ||||| |  | ||| |    ||||| || ||
---------------------------------------------------------------------------gtctcgtt--gtgttcgaacttctctttcctctcttggtctc--gttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtga---agGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggc--gttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
|||||    | |  |       ||  || | |    |     | ||   |   |||    |   |   |      |   | || | |  |||| ||  |    ||  | |      ||  | ||  ||| |  |   |      | | | |  ||| |    | |     ||   |||    ||||||||||||||||||||||||||||| || ||| |  ||||| |  | ||| |    ||||| || ||
gtaagtgctctctctctccctctgtctc-tctggcgtctcgttgactagttgtgttcttatcaagct-tctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcg-ttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtga---agGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG
                             tgataac  putative branch site (score: 2)
                            ttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG