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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattcttaatttttttttctttttatgtattttaaaccccccgttcccgtatctaagagtgtccagatattttctctgatgaagttggtttctttcagctcgtaaattatctaactttggaaactttgttcctgcag

Basic information

species Physcomitrella patens
transcript PP1S37_83V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_83V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT4G14910.3 (Arabidopsis thaliana), 5'ss of exon 7
AGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgt--gattctta-atttttttttctttttatgtattttaaaccccccgttcccgtat-ctaagagtgtccagatattttctctgatgaagttggtttctttcagctcgtaaattatctaactttgga----aactttgttcctgcag
| |||||||||||||| |||||||| || |||||||| |||||||||||||| || |||||||| || | |||| | |||||    || || ||||||||||  || | | | |     |   | | | ||  ||  |  ||      ||  |  |   | |   |  | | ||    | |   | ||||    ||       |     | ||| | |    |  ||    || | ||   ||  ||
AAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGACAATACCAAGgtttgactttgacacacactacacatctcattcatcatccactatttatttgcaaagattcatgataacaaaatccaatttggaaagaagcaaattatggctgg---aaagattgtatgtgataagaaaacaagtctgacgctttag

upper sequence: PP1S37_83V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT4G14910.1 (Arabidopsis thaliana), 5'ss of exon 7
AGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGg--tgattctta-atttttttttctttttatgtattttaaaccccccgttcccgtat-ctaagagtgtccagatattttctctgatgaagttggtttctttc----agctcgtaaatta------------tctaactttggaaacttt-----gttcctgcag
| |||||||||||||| |||||||| || |||||||| |||||||||||||| || |||||||| || | |||| | |||||    || || |||||||||  ||| | | | |     |   | | | ||  ||  |  ||      ||  |  |   | |   |  | | ||    | |   | ||||    ||          || | |||  | |            ||| ||  |  | | |||      ||  |||||
AAAACTCGCATCACATAATAGAAGCGACCTTTAAGGCCTTTGCAAGAGCTCTCCGACAAGCAACAGAGTCTGATCCACGCCGCGGTGGGACAATACCAAGgtttgactttgacacacactacacatctcattcatcatccactatttatttgcaaagattcatgataacaaaatccaatttggaaagaagcaaattatggctggaaagattgtatgtgataagaaaacaagtctgacgctttagatttttgggcatttttgcag
















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|162222109|gb|FC397337.1|FC397337
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|15590622|gb|BI675238.1|BI675238
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGGTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACG
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACG
EST: gi|162153154|gb|FC329560.1|FC329560
EST:     TTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTTTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162196839|gb|FC373894.1|FC373894
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162189058|gb|FC365176.1|FC365176
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|18337884|gb|BJ169908.1|BJ169908
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162222108|gb|FC397336.1|FC397336
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|15261812|gb|BI437122.1|BI437122
EST:     CTGCGTCTAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|208361844|gb|DC950116.1|DC950116
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162208762|gb|FC384898.1|FC384898
EST:     TTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTTTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162271019|gb|FC447424.1|FC447424
EST:     TTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTTTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|19785589|gb|BQ040342.1|BQ040342
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|37838754|gb|BJ596762.1|BJ596762
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|22132850|gb|BQ827398.1|BQ827398
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
EST: gi|162150420|gb|FC326692.1|FC326692
EST:     CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAG                         CTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC
genomic: CTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 25 (upstream exon), 23 (downstream exon)
Score: 5

AGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattctta ... gttcctgcagCTCTAAAGGAGTACTATCACGAGCTTGAGCTTCTGCGACGTAGATTGGATCTATCACGTTTTTTGTAGAAGTAAAGCAGATCTTTGTACCATCAAATGGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAACCATACCAAGgtgattcttaatttttttttctttttatgtattttaaaccccccgttcccgtatctaagagtgtccagatattttctctgatgaagttggtttctttcagctcgtaaattatctaactttggaaactttgttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA