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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcagtcgcacacgttaagcatttagaatcgcttacgatacctttgatattatcttgcaatttatcgaaaagttgagttcctgagctttgggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTATACCAATCTGCGCCGTATCAAGCTGCTACACTTTTCGTGTCGGGGCCCT

Basic information

species Physcomitrella patens
transcript PP1S311_78V6.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S311_78V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
tagcagtcgcacacgttaagcatttagaatcgc-ttacgatac-ctttgatattatcttgcaatttatcgaaaa----------gttgagttcctgagctttgggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTATACCAATCTGCGCCGTATCAAGCTGCTACACTTTTCGTGTCGGGGCCCT
     ||  |  | |   ||| ||| |  || | || |  ||  |||| |  ||    |  |  || ||  |||          | ||   || | | |  | | |    ||||||| || ||||||||||| | ||||||||||||||| || |||||||| || || |||   || ||||||||    || ||||||||  | ||||| |
-----gtatcctatgcctagcctttggtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacac-agATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: PP1S311_78V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ14247 (Selaginella moellendorffii), 3'ss of exon 4
tagcagtcgcacacgttaagcatttagaatcgcttacgatacctttgatattatcttgcaatttatcgaaaagttgagttcctgagctttgggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTATACCAATCTGCGCCGTATCAAGCTGCTACACTTTTCGTGTCGGGGCCCT
                          | ||| |||  ||| |   |||  || |       |||  |      |    ||   |  |||      || ||||||||||||| || ||||||| |||||||||||| || || ||||| ||||||||||||   || || |||||| | ||  |  |  |  | || || |
--------------------------gtatc-cttttgattcacctgagtttgtgc----gttttccaggggatctccttaacgttcttgtttgcgtcagATGACCAACACTATTCAGAAAAAGTTCAAAGTTTCGTCCACGCAGCTACTATACCAATCTTGCCCTTACCAAGCTACAACGTTGATACTTACTGGTCCTT
















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|208385383|gb|DC953044.1|DC953044
EST:     GNTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATT                         ATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
genomic: GTTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATTgtatcctttc ... gggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
EST: gi|208364189|gb|DC950425.1|DC950425
EST:     TTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATT                         ATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
genomic: TTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATTgtatcctttc ... gggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
EST: gi|208373626|gb|DC952451.1|DC952451
EST:     GGCTATTGTGACTACATGTGTAGCACAGATT                         ATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
genomic: GGCTATTGTGACTACATGTGTAGCACAGATTgtatcctttc ... gggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
EST: gi|37845882|gb|BJ603890.1|BJ603890
EST:     TGACTACATGTGTAGCACAGATT                         ATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
genomic: TGACTACATGTGTAGCACAGATTgtatcctttc ... gggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA
EST: gi|208363875|gb|DC943332.1|DC943332
EST:     GTTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATT                         ATGACCAACACCATCCAGAAA-GGTTCAAAGTTTCATCTACACAGCTTCTA
genomic: GTTCCGTAATCTCTTGCTTGGCTATTGTGACTACATGTGTAGCACAGATTgtatcctttc ... gggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattatcttgcaatttatcgaaaagttgagttcctgagctttgggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTATACCAATCTGCGCCGTATCAAGCTGCTACACTTTTCGTGTCGGGGCCCT
                                 ttcctgagc  putative branch site 
              aatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcagtcgcacacgttaagcatttagaatcgcttacgatacctttgatattatcttgcaatttatcgaaaagttgagttcctgagctttgggatgttagATGACCAACACCATCCAGAAAAGGTTCAAAGTTTCATCTACACAGCTTCTATACCAATCTGCGCCGTATCAAGCTGCTACACTTTTCGTGTCGGGGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT