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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggttctgacgcaggttgtcacattcttgtaataggtgttattcagcgttttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT

Basic information

species Physcomitrella patens
transcript PP1S383_1V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S383_1V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 1
-catggttctga---cgcaggttgtcacattcttgtaataggtgttattcagcgtt--ttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT
  || |||  ||     ||  || |  ||||  || ||||   ||   | | | ||  |    |||||||   |     | |||  | | ||||||||        |||     ||  |||||||| || ||||||||||| || || ||||||||||| |||||||| || |||||| |  |  |
ctatagttaggagaattcaaattttt-catttgtgcaataccagtatataaactttgatctgtagggtgtgaaatgaatcgatgtgtatttttctttg--------cagTTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTT
















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|67709710|gb|BJ965526.1|BJ965526
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|18347993|gb|BJ180040.1|BJ180040
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|67717840|gb|BJ968099.1|BJ968099
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|18346096|gb|BJ178139.1|BJ178139
EST:     GTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: GTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|18347116|gb|BJ179162.1|BJ179162
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTT--                         -AGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|208387260|gb|DC933011.1|DC933011
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTT--                         -AGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|100396855|gb|BY953861.1|BY953861
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|100397158|gb|BY972359.1|BY972359
EST:     TTCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: -TCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|67702772|gb|BJ963005.1|BJ963005
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|67717313|gb|BJ967572.1|BJ967572
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|67703834|gb|BJ964067.1|BJ964067
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
EST: gi|18357312|gb|BJ189371.1|BJ189371
EST:     ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAG                         CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT
genomic: ATCTCGTGAAGCCTTTTACCCCACGTTTGGTGGTGTATTGCATCTTTTAGgttagggttt ... tgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgttttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT
                      agctgac  putative branch site (score: 3)
                               tgcttttgtttcttt  putative PPT
                                           tttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catggttctgacgcaggttgtcacattcttgtaataggtgttattcagcgttttaccagggtgtcggagctgaccatgcttttgtttctttgaaatacagCAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - -cacattc