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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagagaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG

Basic information

species Physcomitrella patens
transcript PP1S67_234V6.1
intron # 40
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 39
tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagagaaa----gggagtaccaatgttctttaagc-----ttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG
          | ||| ||  |   |   |  ||||| |    |               |   || | |||  |  ||     || ||   | ||||  | | || ||||| || |||||||| ||||| | |||||||||||| || |||||||||||||||
---------ttctaagaagctcttattgtattgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAG

upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagaga----aagggagtaccaatgttctttaagc-----ttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG-----------------------------------------------
          | ||| ||  |   |   |  ||||| |    |               |   || | |||  |  ||     || ||   | ||||  | | || ||||| || |||||||| ||||| | |||||||||||| || |||||||||||||||                                               
---------ttctaagaagctcttattgtattgctgttcaaaattgtgttttctatttgcctcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA

upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 41
tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagagaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG
|||| | |  | | |   | | ||   |||    ||  | ||             |        |  |     || ||   | ||||  |   ||  |||| || |||||||| ||||| | |||||||||||| || |||||||||||||||
tggcttaagctcttattttattgctgtttgaaattgtgttttctttttgcctcgcttttccctcttctgctcttttttttatattcttgttaattcacagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAG

upper sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
tggcatcat-gtttaaaaatttggcaacttgctgctgcttgttaagagaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG
|    || | ||||| |  | ||      ||      ||| |     || ||  | |   ||| |  |       ||||   ||||  | |     |||||| || ||||||||||| || | ||| ||| ||||||| |||||||||||||||
taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatt-taaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG

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|162279974|gb|FC456160.1|FC456160
EST:     TATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAAGATATTTTCGCAG                         GTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTC
genomic: TATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAAGATATTTTCGCAGgttcagtttc ... ccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG
                                      ttctaat  putative branch site (score: 2)
                           cttattcccttttcta  CT-rich tract
                                    ttttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcatcatgtttaaaaatttggcaacttgctgctgcttgttaagagaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG

- - - - - - - - - - - - - - tgctgct