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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACTACAGAAGAGGAGCTGCTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttcttgatttcggctgatccgaaatcctttttgatgttgcttctgacaactttgttctgtctgaaggaaatggcaacaattgttccagcacccag...

Basic information

species Physcomitrella patens
transcript PP1S87_139V6.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S87_139V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA08G42380.1 (Glycine max), 5'ss of exon 4
GGATACTACAGAAGAGGAGCTGCTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttcttgatttcggctgatccgaaatcctttttgatgttgcttctgacaactttgttctgtctgaag--gaaatggcaacaat-tgttccagcacccag----
|| || |||||  |||| |||||| | || |   ||   ||||||||||||||| | |||||||||| |||||||| |  |||    |  ||      | ||   ||    || ||  | | | ||  |||   ||   ||    |   ||  || ||  |||||        ||    
GGTTATTACAGGCGAGGTGCTGCTCATCTTGGGCTGGGGAAATTCAAGGAAGCTCTGAAAGATTTTCAGCAGgtaactatttg----caacta--taaatatttgttactttgatgtctttaa-aatattgaaatgaaggagcctgggttgaaaataacatgttcatattagtagatca
















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|100358847|gb|BY946718.1|BY946718
EST:     CTTACCTGGCTTTGTTAAA-TTCAAGGAAGCTTTTAAAGATTTTCGGCAG                         GTC-AAAGGATGGTGCCCAATGATCCAGATGCAATCAAGAAGCTTAGGGAA
genomic: CTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttctt ... tatgttttagGTCCAAAGGATGGTGCCCAATGATCCAGATGCAATCAAGAAGCTTAGGGAA
EST: gi|208366737|gb|DC931394.1|DC931394
EST:     CTTACCTGGCTTTGTTAAA-TTCAAGGAAGCTTTTAAAGATTTNCGGCAG                         GTCCAAAGGATGGTGCCCA-TGATCCAGATGCAATCAAGAANCTNAGG-AA
genomic: CTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttctt ... tatgttttagGTCCAAAGGATGGTGCCCAATGATCCAGATGCAATCAAGAAGCTTAGGGAA
EST: gi|22492383|gb|BU052306.1|BU052306
EST:     CTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAG                         GTCCAAAGGATGGTGCCCAATGATCCAGATGCAATCAAGAAGCTTAGGGAA
genomic: CTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttctt ... tatgttttagGTCCAAAGGATGGTGCCCAATGATCCAGATGCAATCAAGAAGCTTAGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACTACAGAAGAGGAGCTGCTTACCTGGCTTTGTTAAAATTCAAGGAAGCTTTTAAAGATTTTCGGCAGgtaatttcttgatttcggctgatccgaaatcctttttgatgttgcttctgacaactttgttctgtctgaaggaaatggcaacaattgttccagcacccag

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