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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttccatttacgcatatcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 8
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgt--aatttcctctttccatt--tacgcatatcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag
|||||||||||| || |||||||| || || ||||||||||| ||||| ||| | |||||  | ||||| || ||| | ||||||||||| || || |||||  ||| | |||  |  |||  | ||  | ||  |||| |||| |  |         || |||   || |||   | | ||  || |                                                                                                          
CAACCCAACTGGAATAGACCCAACTCCGGAACAATGGGAGAAAATTGCAGATGTCATTCAAGAGAAGAAACACATGCCTTTCTTTGATGTTGCATATCAGgtgaaatgttctcactttattatttcgtttttctctgcatgaaa-acaa---------atatcttactgactagcaaatatttctctgcag-------------------------------------------------------------------------------------------------------

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 8
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttccatttacgcatatcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag
|||||||||||| || |||||||| || || || |||||||| ||||| ||| | |||||  | || || |||||| ||||||||||||| || || ||||| |       |||    ||  | |  |  |  |     || | ||      | || |||      || | | ||   |||   ||| |                                                                                                     
CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacg----tttttgcttgagtaccttgtctcct---acgt-atgtatcgcaatatctcttccactgactggtaggctttccttttag----------------------------------------------------------------------------------------------------

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 5'ss of exon 9
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttc--catttacgcatatca---ttgcaggaaacatgatcggcttcgatgtctggatggctaattag---tgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag
|||||||||||| ||||||||||||||||| || ||||  || ||||||||| | |||||| |||||||||||||  |||| || ||||| || |||||||||    ||| || |  ||||| || |||||    || |  || |  | | ||    |    | || |  ||||  |     | || | |||                                                                                                          
CAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAGgtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccag----------------------------------------------------------------------------------------------------------

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttccatttacgcat--atcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag
|||||||||||| ||||| ||||| || || || ||||| |||||||||||| | |||||  | ||||| || ||  | ||||||||||| || |||||||||  || || |||  |||||   ||   |  ||| ||   |     |  | |||  | | ||||  | | |||  ||||||   ||| || | |   ||| |||  |                                                                                    
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgta--ttgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagt-tttgga--gttgatttctgttct---gttgaaatggaaatgaagacaat------------------------------------------------------------------------------------

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|208386964|gb|DC956933.1|DC956933
EST:     TCTTTGATGTAGCTTACCAG                         GGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTTCCGTGAGGAAGTT
genomic: TCTTTGATGTAGCTTACCAGgtaatttcct ... ggtacaccagGGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAG-TTCCGTGAGGAAGTT
EST: gi|162217709|gb|FC393801.1|FC393801
EST:     ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAG                         GGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
genomic: ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcct ... ggtacaccagGGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
EST: gi|162172938|gb|FC348943.1|FC348943
EST:     ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAG                         GGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
genomic: ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcct ... ggtacaccagGGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
EST: gi|208366815|gb|DC940129.1|DC940129
EST:     ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAG                         GGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
genomic: ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcct ... ggtacaccagGGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
EST: gi|162196657|gb|FC373803.1|FC373803
EST:     ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAG                         GGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC
genomic: ATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcct ... ggtacaccagGGTTTCGCCAGTGGGAGCCTGGATGACGATGCTAGTTCCGTGAGGAAGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttccatttacgcatatcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC