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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttggtgtcattgaaaaatggtcgtgagtttttgaatgtcctttttttttccccccttcttctttggttctgatttggttcattattccttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG

Basic information

species Physcomitrella patens
transcript PP1S5_178V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
atttggtgtcattgaaaaatggtcgtgagtttttgaatgtcctttttttttccccccttcttctttggttctgatttggttcattattccttgtca--acagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG
               |   |  || ||     |  |     ||    |  |      ||  ||  ||| | |||||| |  | |  || |    |    ||||| || || ||||||||||||||||| || || || ||  |   | | |||  ||| ||    |||||||||||||| ||||| ||||| ||||||||||
------------gtgagtcttctcctgctccgtccatccgactgcggtgattagaatttgatccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG

upper sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
atttggtgtcattgaaaaatggtcgtg----agtttttgaatgtcctttttttttccccccttcttct-ttggttctgatttggttcattattccttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG
 |||  | |   ||||   |    |      |      ||||     |||| |||    |||   ||| ||| ||||||  ||| |     |   |||    ||||||||||| ||||||||||| ||| ||||||||||  | | | |  |||||   || |     ||| | |||||||||||||| || || || || || |
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggt-----tcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
















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|67508669|gb|BJ941530.1|BJ941530
EST:     CGTCGTCGTTGCGTTCCNGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|208352291|gb|DC906352.1|DC906352
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|208370833|gb|DC936209.1|DC936209
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|67576584|gb|BJ949408.1|BJ949408
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|162232771|gb|FC408178.1|FC408178
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|19789615|gb|BQ041411.1|BQ041411
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|208368697|gb|DC940034.1|DC940034
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|67508011|gb|BJ940885.1|BJ940885
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
EST: gi|67508664|gb|BJ941525.1|BJ941525
EST:     CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGG                         TTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG
genomic: CGTCGTCGTTGCGTTCCGGAAACTTTCAGCTGTCAGCCATGAGTTTCCGGgttagtaatc ... ttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttccccccttcttctttggttctgatttggttcattattccttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG
                       ttctgat  putative branch site (score: 3)
                                      ttattcctt  putative PPT
                                  ttcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttggtgtcattgaaaaatggtcgtgagtttttgaatgtcctttttttttccccccttcttctttggttctgatttggttcattattccttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC