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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 5
----ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
      | ||  |  |   |    |||||||      | ||| ||    ||  |    | || ||||  || ||   |  | |||| ||     | |  || |||| || ||||| || || ||| |||| |||||||||||| |||||||||||||||||||||| || || || ||||| || ||| |  |||| || ||| 
cattggcttgttcccac-atacagtgttttagtcattgaaattttcgaagtggttcactcttaattttgttcat---tctactttcctcgtgaacttttttcagGTTCTAAAAACTCCAGTGTCACTGGATATGCTTGGACGTGTCTTCAATGGTTCTGGGAAACCTATAGATAATGGCCCACCGATTTTACCAGAGGCTTACT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
ttcctgcccgaattg-ttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
||  |    |||||  ||||   | |||| || | |    | |      || | |      ||||| |     |||   | |||| |  ||  |     ||||  | ||||| || |||||| |||||||||||||||| || || ||||||||||| ||||| ||||| || || || || ||| |  | || || ||||
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtc-cacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
ttcctgcccgaattgttttctgttttacc--ttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
||  |    ||||  |||||  ||| |    || | |    ||| |    || |  | |||| |    |  |  ||   | || || | |||  |     ||||  | ||||| || || ||||||||||||||||| || || |||||||||||||| ||||| ||||| || || || |||||  |  | || || ||| 
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaattattgtttttgttcac--agGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 5
ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggttta--gGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC-
 |  |    ||||  ||||   ||||   |    | || ||||| |  | ||||||     |||| |     |||    ||  |   | |  | ||| |  |||  | ||||| || || ||||||||||||||||| || || |||||||||||||| ||||| ||||| || || || |||||| |  | || || |||  
-tgattattgaatcctttttcattttgattctt-tgattttgtttgaat-cagtttaactgttgactcccattttttccttaattattgtttttgttcacaggTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatg-atttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
                       |||   ||   ||         || || |  | |   | |   ||||  | | | ||||       ||  |    |||||  | ||||| || || || ||||| |||||||| || |||||||||||||| ||||| |||||||||||||| || || ||  |  | || || ||| 
----------------------gtttgtttttgctaccaa-----gttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 5
-----ttcctgcccgaattgttt-tctgttttaccttaagtaatgttgttcgtcttcagtttttgattt--gattaatgatttaaatttcttctctttcatgg--tttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
     || |      |||  ||  ||  |    | ||  | |   ||||| |   | | |  |||||||  | ||  ||  ||   |||   |   ||  ||   || ||||  | |||||||| || ||||||||||||||||| || || || || ||||| || || || ||||| || |||||||| |||||  ||||||| ||||
gtaatttaccataaaaatccttcgtccctccagcatttcgcagatttgtt-gaaatgattggttgatttctgcttcctgcattttttttaaaccggtttgtgtctttcagGTTTTGAAAACACCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACC

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
ttcctgcccgaattgttttctgttt--taccttaagtaatgttgt----tcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
        | |    || | || ||  || ||  ||||    | |    ||  ||||  | |||   | |||   | |||        ||||    | |  |  ||||  | ||||| || ||||||||||| |||||||| |||||||| |||||||| |||||||||||||| || || ||||| ||  |  |||| || ||| 
------gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
-ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatt-tcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
 |  ||   | |     ||||| |||    ||||        ||| ||||  |  |||||     || ||   |||   |  |    | |||  | ||  ||||  | |||||||| || ||| |||| |||||||| || || || ||||||||||| ||||||||||| || ||||| || |||||  |||| || ||||
ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggc--aatgaaatgtttgtctggttgaatattttgttgtgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC

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|67576487|gb|BJ949311.1|BJ949311
EST:     ACTTCTGGAATCGATAACAAGCACACCACCATTGAATTCACTGGAGAG                         GTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGT
genomic: ACTTCTGGAATCGATAACAAGCACACCACCATTGAATTCACTGGAGAGgtaatttgat ... catggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC
                  gattaat  putative branch site (score: 3)
                                 tttcttctctttcat  putative PPT
        tttttgatttgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcctgcccgaattgttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC