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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcattttttaactaaacatattgcaatcttgtagtcatttgtttgcttgattttatgggttttagaaagaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTGAAATCCGTGTGCAGTTTAAGGACGCTCCTGGTGATATTTTTAAGT

Basic information

species Physcomitrella patens
transcript PP1S192_39V6.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S192_39V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 11
gtattcattttttaactaaacatattgcaatcttgtagtcatttgtttgcttgattttatgggttttagaaagaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTGAAATCCGTGTGCAGTTTAAGGACGCTCCTGGTGATATTTTTAAGT
               ||| | | | || |      | | ||| | |||   |||   |   | |   |       ||  ||  ||  | ||  |     | | ||| ||  |  |     | |||||| || || |||||  | ||||||||||||||  || |   | ||||||| || || ||||||||||| ||||| ||||||||||| |||||||| |
---------------ctagaaaaaatgaagctgcattgacatctattt--ctgaccctccagttacca-------tt--atcttatctttcagtgcagttaacata-gtaataatcgtgcgctgcagGAGTTCCTTTCATTCTCAAGGCTGGCAAAGCACTGAACAATAGGAAAGCAGAGATACGTGTGCAGTTCAAGGATGCTCCTGGTGACATTTTTAAAT

upper sequence: PP1S192_39V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 11
----------------------------------------------gtattcattttttaactaaacatattgcaatcttgtagtcatttgtttgcttgattttatgggttttagaaagaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgc--agGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTGAAATCCGTGTGCAGTTTAAGGACGCTCCTGGTGATATTTTTAAGT
                                              || ||| ||  |  |     ||||||   ||       | |||      ||   |  ||||    |   | |    ||||   | |      | || | || |      ||    | | ||| ||  ||| || ||||||||| | ||||||||||||||  |  ||||  ||||||| || || ||||| ||||| ||||| ||||||||||| |||||||  |
gtaaatattactcgatgagccattgctcccaatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT
















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|37850762|gb|BJ608770.1|BJ608770
EST:     TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|37821380|gb|BJ579446.1|BJ579446
EST:     GTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCGTCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: GTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|37851014|gb|BJ609022.1|BJ609022
EST:     TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|37841660|gb|BJ599668.1|BJ599668
EST:     GCACATCANCAATGAGCGTTGGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCT
genomic: GCACATCAACAATGAGCGTT-GGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCT
EST: gi|208381262|gb|DC919152.1|DC919152
EST:     TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|162173094|gb|FC349200.1|FC349200
EST:     TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|37850441|gb|BJ608449.1|BJ608449
EST:     TGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
EST: gi|162279045|gb|FC455072.1|FC455072
EST:     TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATG                         GCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG
genomic: TCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattt ... attgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTGAAATCCGTGTGCAGTTTAAGGACGCTCCTGGTGATATTTTTAAGT
                        ttctgat  putative branch site (score: 3)
                                       tcttttatt  putative PPT
                    ttttttctgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcattttttaactaaacatattgcaatcttgtagtcatttgtttgcttgattttatgggttttagaaagaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgcagGCGTACCATTCATCTTGAAGGCTGGCAAAGCTTTGGATTCTCGGAAAGCTGAAATCCGTGTGCAGTTTAAGGACGCTCCTGGTGATATTTTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA