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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgttgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc...

Basic information

species Physcomitrella patens
transcript PP1S97_78V6.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os09g08430.1 (Oryza sativa), 5'ss of exon 5
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgttgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc
|| ||||| ||||| || ||||||  ||| || ||||||||||| |||||||| ||||||||| |  | ||||| |||||||| || || || ||||||||||||||   ||        |||||| |  | |     || ||   || | |  || | |  |     | |  |   |  | |                 
AAAGGTCTGGATGTTGATACTCTTTATGTGTCCCACATTCAAGTTAACCAGGCCCAGAAGCAGAGGCGCCGTACCTACCGTGCTCATGGACGCATCAACCgtaagtt--tgtcaatacctttttgtatgctctttgtagagttcggtgatgct-ttgtctcatgagcaaatgatactttgcag-----------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G119169_T04 (Zea mays), 5'ss of exon 4
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgt--tgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc
|| ||||| ||||| || || ||   ||| |||||||||||||| |||||||| |||||||||||  |  | || ||||| || || ||||| |||||||||||||  |  |   || | | ||   | |  | |   | |  |  | | || | | |  |  | | | |      | |                       
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcagtctgaagttgaagttcgctatgctatgaacaggttactat-ttgcagcttaagatcctacctacctggtgcag--------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G119169_T01 (Zea mays), 5'ss of exon 6
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgttgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc
|| ||||| ||||| || || ||   ||| |||||||||||||| |||||||| |||||||||||  |  | || ||||| || || ||||| |||||||||||||  |   | |     |   |||   | | || |||                                                            
AAAGGTCTTGATGTCGATACCCTCTATGTGTCACACATTCAAGTGAACCAGGCTCAGAAGCAGCGGCGCAGGACCTACCGCGCTCATGGGCGCATCAACCgtaagtcag---tctgaagttgaagttcgctatgctatgaacag--------------------------------------------------------

upper sequence: PP1S97_78V6.3 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G126594_T02 (Zea mays), 5'ss of exon 5
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgttgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc
|| || || |||||||| || ||   ||| || ||||||||||| || ||||| |||||||||||| |  | || |||||||| || || || |||||||||||||     |      | ||    ||||  |   |       | |  |||  ||  |  ||  | || |||||  || |  |  | || | |      
AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagctt--aaca-ttctgtttgcctacctg-gtccag------

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|67695151|gb|BJ955384.1|BJ955384
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67696181|gb|BJ956414.1|BJ956414
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162259989|gb|FC435292.1|FC435292
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67701215|gb|BJ961448.1|BJ961448
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67704010|gb|BJ964243.1|BJ964243
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67696219|gb|BJ956452.1|BJ956452
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162276588|gb|FC451971.1|FC451971
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|67701414|gb|BJ961647.1|BJ961647
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162252890|gb|FC429263.1|FC429263
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
EST: gi|162259990|gb|FC435293.1|FC435293
EST:     GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACC                         CTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG
genomic: GGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggc ... cgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGGTCTCGATGTGGACACTCTTGTTGTATCACACATTCAAGTCAACCAGGCGCAGAAGCAGCGAAGACGTACTTACCGTGCCCACGGGCGTATCAACCgtaagttggcgttgtcggacttttgttttttttcctctgacttttctgtttcggttatattttcgatcagttctgggtgacggcaggagtgccgagtctc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA