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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatattgcatctaatttgtaagttgccttcaattgtgttcatattcttcttcacaatctgagtcttgagatgacaattcatatttcttttgtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAATCCACAGGATGCGGCGT

Basic information

species Physcomitrella patens
transcript PP1S505_16V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S505_16V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g33180.1 (Oryza sativa), 3'ss of exon 5
gtatgatattgcatctaatttgtaagttgccttcaattgtgttcatattcttcttcacaatctgagtcttgagatgac-aattcatatttctttt---gtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAAT-CCACAGGATGCGGCGT
                    | |   ||   |||||   | ||  | || | ||  |     ||| | |||  || ||  | ||  |  ||||||      ||| |||||||||||||||||||| | ||||| || ||||||||||| ||  |||| || || || ||| | |||||||||||  | ||  || || || ||     |  
-------------------gtatgtttttggttcaaacttattgttgttttgctctattccttgatttttgccatcactgactctgacatctttttaaaaatttttgcagTGGAAATGTTGTGATATTCATGTCAAGGAATTTGATGAATTTATGGAGATCCCTCCGTGCACAAAGGGTTGGCACAATGCTGATGCCGCATGAATTTTCA-

upper sequence: PP1S505_16V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G156105_T01 (Zea mays), 3'ss of exon 2
gtatgatattgcatctaatttgtaagttgccttcaa-ttgtgttcatattcttcttcacaatctgagtcttgagatgacaattcatatttcttttgtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAAT-CCACAGGATGCGGCGT
||||| |||   ||| || || || |||   |||   || |||  |||    |   | | |||                || || ||  ||| || ||     |||||||||||| |||||| | ||||| || ||||||||||||||  |||| ||||| |||||| | || ||||||||| | ||  || |     ||     || 
gtatg-tatc-tatcaaagttatatgttagtttctgcttctgtaaataactattcccgccatc-------------actaaatcctaggtctgttctt-----gcagTGGAAATGCTGTGATATTCATGTCAAGGAATTTGATGAGTTTATGGAGATACCTCCATGCACAAAAGGTTGGCATAATGCTGATGCGGTGTGAATTCACG-

upper sequence: PP1S505_16V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G868908_T01 (Zea mays), 3'ss of exon 4
gtatgatattgcatctaatttgtaagttgccttcaat---tgtgttcatattcttcttcacaatctg--agtcttgagatgac-aattcatatttcttttgtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAATCCACAG-GATGCGGCGT
      ||| | || || ||      ||   || ||    | |||| || |    ||    || | |  | ||| |  ||  | ||  |  || ||| || | ||  ||||||||||||| |||||||| ||||| || || ||||| |||||  |||| |||||  ||||| | |||||||||||| | ||  || |   | ||     || 
-----gtat-gtatatatttgaaggatttatttgaagctatatgttgatttctgcctctgtaaacagctattctcgccatccctaaaccccatatctgttctgttcttgcagTGGAAATGCTGTGATGTTCATGTCAAGGAGTTTGACGAGTTTATGGAGATACCTACATGCACAAAGGGTTGGCATAATGCTGATGCGGTGTGAATTCACG-

upper sequence: PP1S505_16V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G38720.1 (Glycine max), 3'ss of exon 4
-----------gtatgatattgcatctaatttgtaagttgccttca----attgtgttcata-ttcttcttcacaatctgagtcttgaga-tgacaattcatatttcttttgt-----ttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAATCCACAGGATGCGGCGT
           ||||   ||| | |  ||| |    ||| | || |    ||  || |  |  || |   |    || ||| |   |||| | ||| || || |||| ||| |     | || |||||||||| || |||||| | |||||||||||||||||||||||  ||   || || || ||||| ||||| |||||| | ||  ||||| ||       |  
gtcagtattgagtatt-cattcctttgaatgttctcgtttctttaataaaataatgcttgtggttgtgacttgtgatatgatttcagagaattacattttatttttcctttatcacattattttgcagTGGAAGTGCTGTGATATTCATGTAAAAGAATTTGATGAGTTTATGAGCATTCCTCCGTGCGCAAAGGGATGGCATAATGCGGATCCAGAGTCCTGATCAC

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|208374740|gb|DC948684.1|DC948684
EST:     CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGG                         TGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
genomic: CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGGgtatgatatt ... ttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
EST: gi|18338838|gb|BJ170863.1|BJ170863
EST:     CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGG                         TGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
genomic: CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGGgtatgatatt ... ttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
EST: gi|208367662|gb|DC955007.1|DC955007
EST:     CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGG                         TGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
genomic: CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGGgtatgatatt ... ttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
EST: gi|208394738|gb|DC924069.1|DC924069
EST:     CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGG                         TGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA
genomic: CTTGCAATTATCACCCTGGCCCTGCGGTGTTTCACGATCGACTTAGAGGGgtatgatatt ... ttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcacaatctgagtcttgagatgacaattcatatttcttttgtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAATCCACAGGATGCGGCGT
                                 tatttcttttgttttt  CT-rich tract
                           aattcatatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatattgcatctaatttgtaagttgccttcaattgtgttcatattcttcttcacaatctgagtcttgagatgacaattcatatttcttttgtttttgtgcagTGGAAATGTTGTGATGTGCATGTAAAAGAATTTGATGAGTTCCTGGAAATACCCCCATGCGCCAAGGGTTGGCATGACGCCAATCCACAGGATGCGGCGT

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