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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGAACAATCGAGCTTTGCTGCTGGATCCCTGATTCCCCTGTCGCAGCGAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgttttgcattacccagcttttgttttgctgtgttttgtattgctttctatgcattccttctcattgtcgatcggtgaatccttttgaggttt...

Basic information

species Physcomitrella patens
transcript PP1S85_160V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G092459_T02 (Zea mays), 5'ss of exon 1
TCGTGAACAATCGAGCTTTGCTGCTG--GATCCCTGATTCCCCTGTCGCAGCGAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatg-tttgttttgcattacccagcttt---tgttttgctgtgtt--ttgtattgctttctatgcattccttctcattgtcgatcggtgaatccttttgaggttt
 | |   |||| |  |   ||  |||  || |    |  | | || |||  ||  ||||| ||       || || ||||||||||||||||| ||||||||||| |   |   |  |  | || || | |    |    |  | |      ||    |   ||    ||    ||  | | ||| |||  | |              
GCCTCTCCAATTGC-CACCGCCACTGACGAGCGACCACACGCTTGGCGCC-CGCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctccctccctctccctagatctgcgcgcgaaggcgcgacgacggtgagtcacgctgctgatctgctcctactctcgctcgcggcag-------------
















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|100404540|gb|BY973629.1|BY973629
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|18351206|gb|BJ183257.1|BJ183257
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100397452|gb|BY972506.1|BY972506
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTACTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|67570355|gb|BJ943179.1|BJ943179
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100448162|gb|CJ972461.1|CJ972461
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|208359135|gb|DC930467.1|DC930467
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100440187|gb|BY980439.1|BY980439
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100365851|gb|BY967178.1|BY967178
EST:     GTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGAACAATCGAGCTTTGCTGCTGGATCCCTGATTCCCCTGTCGCAGCGAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgttttgcattacccagcttttgttttgctgtgttttgtattgctttctatgcattccttctcattgtcgatcggtgaatccttttgaggttt

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT