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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctcccactattatctacatgttaataggggcatcattttctgatattgccgtttaattaatcttcgttttatttttgtttttttccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG

Basic information

species Physcomitrella patens
transcript PP1S83_83V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 7
----------------------gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctcccactattatctacatgttaataggggcatcattttctgatat-tgccgt---ttaattaatcttcgttttatttttgtttttt---tccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG
                       |||  |  |  || | ||  || | ||  | |      |||   |  || | ||    |||||| ||  | |   |      |  ||||  |  ||  ||||     ||  ||| ||     ||||||| || || ||   | |||    |||||  | || ||||||||||||||||| |||||||| || ||||| ||||| || || || || || |||||  |||||||||| || |||||||||    
gttcgttttcatttcctttatgttgaattatataaataccacctgttagtacttgctaacaattgtttctatcgttctt--tattatttaattatatgtttaactactatttattagtacatgccagtaattgtttattcgcttatttatttctggttattgtttacctgttgcagGAGCTTTTATATGACAAGGAGAAGCTGCTTGAAAATGGGGACCGATGGGAGACTGAAATTGCAGAGAACCTGAGATCTGAAAGCCTTTACCGCTGAAATT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G31520.1 (Glycine max), 3'ss of exon 8
---------------------gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctccc-actattatctac-atgtt-aataggggc--atcattttctgata-ttgccgtttaattaatcttcgttttatttttgtttt---tttccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG
                      |||  |  |  || |  || || | ||  | |      |||   |  || | ||   | |||||  ||  ||||| |||        || | |   ||  | |    ||||| ||| |  |   ||||||| || ||    |||  ||    |||||  | || ||||||||||||||||| |||||||| || ||||| ||||| || || || || || |||||  |||||||||| || || ||||||    
gttcgtttcatttcctttatgttgaattatataaatacgatctgttagtacttgctaacaattgtttctattgttctttattattaattattatgtttaattactatttattagtacatgccagtaattgtttatttacttatttctttatttctggttattgtttatctgttgcagGAGCTTTTATATGACAAGGAGAAGCTGCTTGAAAATGGGGACCGATGGGAGACTGAAATTGCAGAGAACCTGAGATCTGAAAGCCTTTATCGCTGAAATT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G79010.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctcccactattatctacatgttaataggggcatcattttctgatattgccgtttaattaatcttcgttttatttttgtttttttccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG
                                                          || || |  |||| ||         |  | |||  ||       | ||| | ||          ||||||||| | ||| ||   | ||||| |  | |||||||| |||||||||||||| || || || || ||||| |||||||| ||||| || ||  | || || |||||||||||||||    
--------------------------------------------------------gtctgtttttcacattttctagaccctaataattttcgaggca--tgcttattgaa----------atttttgttatattctctatgatagGAACTTCTCTATGACAAAGAGAAGCTTCTTGAGAATGGAGATCGATGGGAGACAGAGATTGCTGAGAATCTGAGGTCGGAGAGTCTCTACCGCTGAACCA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0063g02550.t01 (Vitis vinifera), 3'ss of exon 7
gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctcccactattatctacatgttaataggggcatcattttctgatattgccgtttaattaatcttc---gttttatttttgtttttttccctcga-acagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG
                                                              | | ||    |   |   | |   |  |  ||| | ||||    | ||  |       |  | |||||| | ||  |   ||    |||||  |  ||||||| || |||||  | ||||| ||||| || ||||||||||| ||||| || || |||||  || ||||||| ||||||||||||    
-------------------------------------------------------------gtctgtaagcatccttctcgccgctagataatga-actgcccagcagttggttccaaaagaatgatttttatcttcctgtatcattgcagGAGCTCCTGTATGATAAAGAGAAATTGCTTGAGAACGGGGATCGCTGGGAAACCGAGATTGCAGAGAACCTCAGAGCTGAAAGCCTCTACCGCTGATAAT

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|162226492|gb|FC402446.1|FC402446
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTG
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTG
EST: gi|208365908|gb|DC951087.1|DC951087
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|162226685|gb|FC403770.1|FC403770
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|100407453|gb|BY991709.1|BY991709
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|208391815|gb|DC937991.1|DC937991
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGA
EST: gi|208356711|gb|DC902543.1|DC902543
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATG
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATG
EST: gi|67719791|gb|BJ970050.1|BJ970050
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATNGTTGTATGACAAGGAGAAGCTTCTTGA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGA
EST: gi|208389974|gb|DC938029.1|DC938029
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAAACTCATGAG                         GAATTGTTGTATGA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGA
EST: gi|208398252|gb|DC916419.1|DC916419
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|208365816|gb|DC951051.1|DC951051
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|67692407|gb|BJ952640.1|BJ952640
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
EST: gi|162226684|gb|FC403769.1|FC403769
EST:     ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAG                         GAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA
genomic: ACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACGGAGACTCATGAGgtgagcttca ... cctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattgccgtttaattaatcttcgttttatttttgtttttttccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG
              aattaat  putative branch site (score: 3)
                    tcttcgttttattttt  CT-rich tract
           tttaattaatcttcgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttcacgaagaacatgtggtggttatggtccggtattccgtagatagctcccactattatctacatgttaataggggcatcattttctgatattgccgtttaattaatcttcgttttatttttgtttttttccctcgaacagGAATTGTTGTATGACAAGGAGAAGCTTCTTGAAAACGGTGACCGCTGGGAAACAGAGATAGCTGAAAACCTTCGATCTGAAAGTCTCTACCGCTGAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA