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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcattttttttttttttttttttttttttttttttctagcttgaatgtagttttgatcatgagtgctctaaacatgtgattgtgttgactttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTTAAGGGAAAATCTCTTGC

Basic information

species Physcomitrella patens
transcript PP1S50_114V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S50_114V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 9
atgcattttttttttttttttttttttttttttttttctagcttgaatgtagttttgatcatgagtgctctaaacatgtgattgtgttgactttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTTAAGGGAAAATCTCTTGC
     |||| | | ||||  || | |  |   |  ||||    | | | |   ||   |  | | | || |     | |   | | ||  ||      || | || ||||  ||       || ||||||||||||||||||||| |||| || |||||||||||  |
gcaagttttatgtattttacttctgtactcactaattctgtactaattttg--ttaagtgctcatttctttttttttttccctctttt--ctacaagcagTTGCACATTGCCTTTTGCATTTTAGCTGCAGTTGCTCCACCAATTATCTTCAAAGGAAAATCTCTCAC

upper sequence: PP1S50_114V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 9
atgcattttttttttttttttttttttttttttttttctagcttgaatgtagttttgatcatgagtgctctaaacatgtgattgtgttgactttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTTAAGGGAAAATCTCTTGC
           |||| | ||||||  || | |  |  |||  |      || |||||      |||||||    | | |     | ||  ||      || | || ||||  ||       || || |||||||||||||||||| |||| || |||||||||||  |
------gcaagttttatcttttttacttctgtagtccctaattctgtactaattttgtg---aagtgctcatttctttttcccctcttt-ctacaagcagTTGCACATTGCCTTTTGCATTTTAGCGGCAGTTGCTCCACCAATTATCTTCAAAGGAAAATCTCTCAC
















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|208349681|gb|DC917859.1|DC917859
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|67701518|gb|BJ961751.1|BJ961751
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|208394706|gb|DC903962.1|DC903962
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|67695428|gb|BJ955661.1|BJ955661
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|208380999|gb|DC919881.1|DC919881
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|208375107|gb|DC944846.1|DC944846
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
EST: gi|162258284|gb|FC434683.1|FC434683
EST:     GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGT                         CTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT
genomic: GTCTGACAGTGCCCTGAAGTTCGGTTGGTTCTTCCTCTTCTATTGTgtaagtgttt ... ctttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtagttttgatcatgagtgctctaaacatgtgattgtgttgactttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTTAAGGGAAAATCTCTTGC
                                       tgttgac  putative branch site (score: 3)
                                              tttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcattttttttttttttttttttttttttttttttctagcttgaatgtagttttgatcatgagtgctctaaacatgtgattgtgttgactttgtatagCTCCATATTGGTTTCGTTGGATTGGCTGCAGTTGCTCCACCAATTTTCTTTAAGGGAAAATCTCTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG