Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTTCTCGCAAGAATCCTTACCTGGTAGTCTTTCCTTGTGATTCAGACTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgctttatctacctgcctaatgaaacttagtttctctcttttgcattatcttgtgttcatcgtatctcaaaaagaagcgtccttgtattttatattgtatttcgtgcattgaaagaagttgatttcgtgcag

Basic information

species Physcomitrella patens
transcript PP1S134_26V6.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S134_26V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
GTTATTTCTCGCAAGAATCCTTACCTGGTAGTCTTTCCTTGTGATTCAGACTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgctttatctacctgcctaatgaaacttagtttctctcttttgcattatcttgtgttcatcgtatctcaaaaagaagcgtccttgtattttatattgtatttcgtgcattgaaagaagttgatttcgtgcag
                                                  |||||||||  |||||||||||||| || || ||||| ||||| ||||||||| |  ||   | ||                 |||| | ||    |||| |   | | |    || |  |          |    || || |   |  | |  |  || |                            
-------------------------------------------------GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgta-gcatgtcctttc---------------gtttagctcctgcgctttgtacagtttggaa--cagctaactatgggctcacatttctttttcactactgtgatgattag----------------------------
















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|162189955|gb|FC365619.1|FC365619
EST:     CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|162259126|gb|FC435185.1|FC435185
EST:     CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|162272666|gb|FC448292.1|FC448292
EST:     CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|162189954|gb|FC365618.1|FC365618
EST:     ATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: ATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|37843892|gb|BJ601900.1|BJ601900
EST:     CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|37845078|gb|BJ603086.1|BJ603086
EST:     CTGCCATTGCAAATTNTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
EST: gi|162235645|gb|FC411390.1|FC411390
EST:     CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAG                         GCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT
genomic: CTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgc ... tttcgtgcagGCCCTCAAGCTAGGGCAACTACCCTCTGACATTGAACTCCCTGGAGTCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTTCTCGCAAGAATCCTTACCTGGTAGTCTTTCCTTGTGATTCAGACTGCCATTGCAAATTCTCAGACACTCGAAGAAGTTGCCAGGCTGGAAAAGgtatgagtgctttatctacctgcctaatgaaacttagtttctctcttttgcattatcttgtgttcatcgtatctcaaaaagaagcgtccttgtattttatattgtatttcgtgcattgaaagaagttgatttcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA