Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgcttaatcttttgggggtatatttaaacttactttgccctttgtttaccttataacataccttgtgcttttggaattctcatctgacataacctcaacgttgtttttgccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG

Basic information

species Physcomitrella patens
transcript PP1S89_154V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S89_154V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 11
-----------------------------------gtatgttgcttaatc---ttttgggggtatattt----aaacttactttgcc-------ctttgtttaccttataa--------------cataccttgtgcttt--tggaattctcatctgacataacctcaacgttgtt--tttgccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG
                                   ||   ||| ||  |    | | |  ||  |||||    |  | |  |||| |       ||||    |||||| ||              ||||| |  |  |    || | ||  | |   |   |   |  |  || ||  ||      | ||| ||||| ||||||||     | ||   | |||| ||    || |||||  | || |||||| | ||||||||||| ||||||||||||| ||||||| ||
gtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTG

upper sequence: PP1S89_154V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------gtatgttgcttaatcttttgggggtatatttaaacttactttgccctttgtttacc---ttataacataccttgtgcttttggaattctcatctgaca--taacctcaacgttgtttttgcccc----accagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG
                                                                    |  ||||   |||    |     ||  || | | |||  |   || |     || |    |  |  |||| |      ||| |  | ||  |    ||  |||  |  |  |  | |||   |     | ||| ||||| ||||||||     | ||   | |||| ||    || |||||  | || |||||| | ||||||||||| ||||||||||||| ||||||| ||
gtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgt-catgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcagCTGTCCGGAGTTGGAAGAACTTGTAAATATTTGTCGTAACAATGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTG

upper sequence: PP1S89_154V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttgcttaatcttttgggggtatatt-taaacttactttgccctttgtttaccttataacataccttgtgcttttggaattctcatctgacataacctcaacgttgtttttgccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG
                       |||  |  |||| ||||| |            ||||    | ||||   || | |||    | | |      |   | |   | | |||||      |  || || || ||||||||     | ||     |||||||   ||| || ||  | ||||||||| | ||||||||||| |||||||||||||  |||||  ||
----------------------agtacgtgataaaattactctctgaacaaaaatcctttgcccctaccaattg-tgttgatcatattactcataaaggcttt--cctggttttcctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCTTGGAGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCAGTTGCCTTG

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|162189012|gb|FC365130.1|FC365130
EST:     GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
EST: gi|208388403|gb|DC957041.1|DC957041
EST:     GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
EST: gi|162195375|gb|FC369310.1|FC369310
EST:     GCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
EST: gi|162272814|gb|FC448802.1|FC448802
EST:     GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
EST: gi|208385544|gb|DC956700.1|DC956700
EST:     GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GAGCTCATGAACGAGAGCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
EST: gi|162195376|gb|FC369311.1|FC369311
EST:     GCCATGCGAGCTGCAGCCTTCTGTACGAATGCAG                         TTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT
genomic: GCCATGCGAGCTGCAGCCTTCTGTACGAATGCAGgtatgttgct ... gccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttttggaattctcatctgacataacctcaacgttgtttttgccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG
                       acataac  putative branch site (score: 3)
                                        tttttgcccc  putative PPT
                                     ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgcttaatcttttgggggtatatttaaacttactttgccctttgtttaccttataacataccttgtgcttttggaattctcatctgacataacctcaacgttgtttttgccccaccagTTGTCCTGAGTTGGAGAGCTTAGTGGGTCTTTGCCGACGTAACGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT