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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaagggatagttaatccgccaacatggatctcgttttcatactcgtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG

Basic information

species Physcomitrella patens
transcript PP1S425_2V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 1
---ggaagggatagttaatccgccaacatggatctcgttttcatactcgtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
     |     ||| | |        | |  ||          |||   ||  | ||    ||    |     |  |    || |   ||||  |   | |||||||||| |||||||| |||||||| |||||| |||| || ||  | || || || ||||||||||||||||||||  | ||||| || || ||||   |
tatccatttcttagatgaaggattt-cttcaatgctagacaagtacaaatgcacaattggttgcttctttgtgtgttgatctttatgctgtt--ttgtttcagTTGACATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCG

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 3
ggaagggatagttaatccgccaacatggatctcgttttcat--actcgtgtt-cgatgatgtgaaattcaaattaattcatttcacattgttggtg-----aatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
         | |  || |   |    |  | |||||||  |  |    ||||    |||  |  | || |||||  || |   |   | | |||||       ||||||||| || ||||| || ||||| || |||||  ||||| | ||  | || ||||| ||| | |||||||||||||| ||||| ||||||||||||  || 
------tgaattagattcaatagt-cgtttttcgttttgctgaatcgatgttattctgaattttagttgaaatttcttaaaaac-tgtagctggtgtttcctctgcagTTGATATAATCTCAGCGATTGAATTTGATAATTCTGGAAACCATCTTGCTACTGGGGACCGTGGAGGACGTGTTGTTCTTTTCGAGAGAACCGATACCAA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
-ggaagggatagttaatccgccaacatggatctcgttttcatactcgtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
 |  | |   | ||| |  | ||  |||         ||   |   || ||   |   | | | |     ||   | |    ||       ||   |||||||||||| || |||||||||||||| || ||||||||||| ||  | |||||||| ||  | || ||||| || ||  | ||||| || || ||    ||
cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttt-tgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG

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|162150295|gb|FC326380.1|FC326380
EST:     ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAG                         TTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
genomic: ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgtatgttatg ... gtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
EST: gi|100389123|gb|BY952327.1|BY952327
EST:     ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAG                         TTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
genomic: ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgtatgttatg ... gtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
EST: gi|162255330|gb|FC432056.1|FC432056
EST:     ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAG                         TTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
genomic: ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgtatgttatg ... gtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
EST: gi|100386449|gb|BY951245.1|BY951245
EST:     ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAG                         TTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA
genomic: ATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgtatgttatg ... gtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
                      aattaat  putative branch site (score: 3)
             tgaaattcaaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaagggatagttaatccgccaacatggatctcgttttcatactcgtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA