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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaccttcaagtgttcgcaattgttgcatttattatattttgtacccccaccactgtcatctcttaagattgtgttagtactgttgcacaatgtgctctttagcgtattgacatggtgcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTTTGGAAGAGACATCATTTCGTGGTCGCACAGCAGATTTCTTCTTTATGCT

Basic information

species Physcomitrella patens
transcript PP1S226_55V6.1
intron # 3
splice site 3'
intron type U2

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|100406309|gb|BY955567.1|BY955567
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
EST: gi|208375016|gb|DC956412.1|DC956412
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
EST: gi|100445439|gb|CJ975588.1|CJ975588
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTT-CCACATGTTCTTTCTGGCANG-TATTGTAAA
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAA
EST: gi|37851348|gb|BJ609356.1|BJ609356
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTCCCACATGTTCTTTCTGGCAAGGTATTGTAAACTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTT-CCACATGTTCTTTCTGGCAAGGTATTGTAAACTT
EST: gi|100449404|gb|CJ973703.1|CJ973703
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
EST: gi|208386348|gb|DC932844.1|DC932844
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTCCACATGTTCTT-CTGGCANG-TATTGTAA-CTTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT
EST: gi|100361762|gb|BY947614.1|BY947614
EST:     TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTG                         ATTTGGACTTCCTTTTTCACATGTTCTTTCTGGCANGGTATTGTAAACTTT
genomic: TTATCAAGTCTGGAGACTCATCACCAATTTCTTTTACTTTGGCAAACTTGgtatttacct ... gcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttagtactgttgcacaatgtgctctttagcgtattgacatggtgcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTTTGGAAGAGACATCATTTCGTGGTCGCACAGCAGATTTCTTCTTTATGCT
                                 tattgac  putative branch site (score: 2)
                                            tgccctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaccttcaagtgttcgcaattgttgcatttattatattttgtacccccaccactgtcatctcttaagattgtgttagtactgttgcacaatgtgctctttagcgtattgacatggtgcccttgcagATTTGGACTTCCTTTTCCACATGTTCTTTCTGGCAAGGTATTGTAAACTTTTGGAAGAGACATCATTTCGTGGTCGCACAGCAGATTTCTTCTTTATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT