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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

Basic information

species Physcomitrella patens
transcript PP1S28_21V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
------------------aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
                    | |  | |||   ||||      | | | ||     | |     |    ||   ||         |    | | |    ||  |  || || |  ||||||||  ||||||||||||||||||| || |||||||||||||| ||||| || || |  ||||||||||| ||| ||||
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactt-tcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
------------------aatgcctttttaccatttatccgagatattcatcaca-gactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
                    | || | |||   ||||      | | | |||    |  |     |   ||   |||    |    ||   | | |  ||    |  ||  | |   |||||||  ||||||||||||||||||| || |||||||||||||| ||||| || || |  ||||||||||| ||  ||||
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctt--tagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
------aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaa----gcatagaaagagaatccttatttaccgtctcgtga-ttgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
        |   ||   |  || ||   |   || || |       | || ||    ||    ||||    | |  ||    |       | |    | |||   |   |||||||  ||||||||||||||||||| || || |||||||| || ||||||||| | |  ||||||||||| ||  ||||
gtgatttttcagttcacagaatataaatgccttactctttttgtgttacatcttgctaactttgcatgcttacaatatttgaaccattattattaaaacttgctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
--aatgccttttt------accatttatccgaga--tattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattga--cgtgcc-------agATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
  |||  ||||||      |  | |||||   |   || || |       | |  |      | | | | |     |   || || | |   || ||||| |  | |||        |||||||  ||||||||||||||||||| || || |||||||| || ||||||||| | |  ||||||||||| ||  ||||
gtaatttctttttcagttaataaattatcaaggcattactccttttgtgttacttccttgctaacttggtatacttacaatttttgaactgttc-tgattaaaacttgctctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
-aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
  | |  | ||| |  ||  ||| |||  |   |     ||||  | | |||  | ||    |   | |     |      | |  | |||        ||||| |  |||| |||||||| |||||||| |||||||||||||| ||||||||  | | |||||| ||||| ||||  ||
gtaagtttgtttgcttttcttcctagac-tatgttgtgtactgtga-tgatattgaatgtctacttattttgcttccttttttttttcatttg---attagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaag----catagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
  |   | ||||  ||  |   | | | | | |   |   || |||    |||     ||||   | | || | |   | |  || |   |  | |  |   ||||| |  |||||||||||||||||||||| || |||||||||||||| |||||| | |  || |||||||| || | |||
-gttagtgtttataat--aagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatat-agATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgat-tgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
              | |  | |   | |    |   |      ||||  |||  | | ||||||||    | | |     | | ||  | | |  |   ||||| |  |||||||||||||||| ||||| || ||||||||||||||||||||| | |  || | |||||| || | |||
-----------gttagtgttgcagtaaaacagttttatttaaaaacttgtaa--cctggaaagagatatgtaactgtgtatttggtcttataatatat-agATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG
                                         gattgac  putative branch site (score: 3)
                         ttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaagcatagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG