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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaggatttccaagtatgtactattcaatggtatgagatgcgaatttgtagattaggtggtacatgttattgataagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG

Basic information

species Physcomitrella patens
transcript PP1S39_347V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_347V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G17960.1 (Glycine max), 3'ss of exon 3
------------------------------------gtcaggatttccaagtatgtacta---ttcaatggtatgagatgcgaatttgtagattaggtggtacatgttattga--taagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG
                                         | |      ||   | ||    ||  ||| ||   | | |   | | ||  |  ||| ||   |||| ||||  |  | || | |      ||    |||| ||||| || |||||||| ||| | || || || || ||  || | || || ||||| |||||||| ||||||||||||||||||||  ||||||||||
gtgagtgtttgttaattttaactttaatttcactattctttgttcctttggtgaatgctgagtttttatgttacttgttacttttatctatttgtggttgtctttgttcttgaattttgagtgttggctgtctc----cagCATCGCAGTCTGTGAAGAAGATTATTGAAATTAATCCGTATATGCTTGGGACAATGGCTGGAGGTGCTGCTGATTGTCAGTTTTGGCACAGGAATCTTGG

upper sequence: PP1S39_347V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 3
gtcaggatttccaag-tatgtactattcaatggtatgagatgcgaatttgtagattaggtgg-tacatgttattgataagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG
 |||     || ||  | || || ||  ||| |   ||  |       | | |||    ||  ||  |||| || ||     |       ||||  || |||| || ||||| |||||||||||| | || || || |||||| || | ||||| ||||| ||||| || |||||||| |||||||||||  | ||| | ||
ctcatctgatcaaaactttgaaccatgaaatagggagatcttttggactttggatgcattgcctatttgtt-ttcattgtcttccttccttatttttg-cagCATCACAATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGG

upper sequence: PP1S39_347V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ04804 (Selaginella moellendorffii), 3'ss of exon 2
gtcaggatttccaagtatgtactattcaatggtatgagatgcgaatttgtagattaggtggtacatgttattgataagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG
                                               |     ||   | ||   |||   |  |   |  |||||   ||   | ||||| || || |||||||||||||||||||| |||||||| ||  |  |||| || ||||| || ||||| || ||||||||||| |||||  | ||||||||
----------------------------------------------gtaagtgtttcttcgtgtttgtctctacttgtg--atcgagtgatctctcgcagCATCCCAGTCGGTGAAGAAAATTCTGGAAATCAACCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGG

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|208375166|gb|DC945316.1|DC945316
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|7067446|gb|AW497301.1|AW497301
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|19785617|gb|BQ040349.1|BQ040349
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|67697970|gb|BJ958203.1|BJ958203
EST:     CTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: CTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|67727381|gb|BJ977640.1|BJ977640
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|208365548|gb|DC954789.1|DC954789
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|67693026|gb|BJ953259.1|BJ953259
EST:     GACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: GACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|7148045|gb|AW509967.1|AW509967
EST:     TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGGCGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|208395764|gb|DC924230.1|DC924230
EST:     TGACTCGCGTGCCAGCATGGGCAANTACATTT                         CCTCGCAATCNGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: TGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|208368061|gb|DC947621.1|DC947621
EST:     GCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: GCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
EST: gi|208359388|gb|DC954241.1|DC954241
EST:     CGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTT                         CCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA
genomic: CGTCATCGTGGCTGCTGACTCGCGTGCCAGCATGGGCAACTACATTTgtatgtccgc ... ttcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtagattaggtggtacatgttattgataagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG
                       tattgat  putative branch site (score: 3)
                      ttattgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggatttccaagtatgtactattcaatggtatgagatgcgaatttgtagattaggtggtacatgttattgataagggtatcgatatattcatggcagCCTCGCAATCGGTGAAGAAAATTCTGGAGATCAACCCCTACTTGTTGGGCACTATGGCGGGAGGTGCCGCTGATTGTCAGTTTTGGCAACGGAATCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT