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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttgaacagtatccatattgattcatcgttggttttattggtag

Basic information

species Physcomitrella patens
transcript PP1S58_256V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttgaacagtatccatattgattcatcgttggttttattggtag
 || |||||||| ||||||||||| ||||||||||| || |||||  | |||||||| || ||  | ||  | ||  | |||| ||| ||||||||||||||     | |  ||| |||    |    |    || ||    |    ||  |   |    | || |   | |  || ||  || ||| ||  ||          
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttt-tgtttgttttatagcttttcattatgtgat----tatgtatgatttatatgtt--tttatcatttattag--------

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 3
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc--gttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtc--ttttgaaca-gtatccatattgattcat-cgttggttt---tattggtag
  | |||||||| ||||| ||||||||||||||| | || | |||| |||||||||| |||||| | ||| ||||||| |||| |||| |||| || ||||| |   ||   |||| || |||| |    |  |  |  | ||||    ||||    ||     |  |  || || |   | |||||  ||  ||  || |    ||  ||||
ATCCATGGTGCAACAAGCAATGCAGTATATTGATCAGACACTAGACATAGAAACTCGGATTGAGCTTATTAAGACTCTAAACAATGTAGCTGCTGGAAAGgtgcggattagagttggct-attgttgttgttgttgtagttatatttgcttgaatcttgatcactccgtgcaagtttttttcttgatgaatatgtgtgtgtgagcatgtgtag

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 3
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttgaacagtatccatattgattcatcgttggttttattggtag
  | |||||||||||||| ||||||||||| ||| | || |||||| | |||||||| || ||| | ||  |||| || |||| ||||||||| || ||||| |        | |   | || |    || |||| || ||| |   || | ||     || ||   | | |   ||    | |||  ||   | ||| |    
ATCCATGGTGCAGCAAGCAATGCAGTATATCGATCAGACACCAGACATTGAAACTCGGATAGAGCTTATCAAGACGCTGAACAATGTATCTGCTGGAAAGgtgcgaa---actatgaaactgatggtgtattctttataataac---ttcatca-----ttctgtgtaat-tgtttaccattgcatt-ttacatgtatag----

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttga-acagtatccatattgattcatcgt--tggttttattg-gtag
||| ||||| |||||||||||||||||||||||  | || || ||  | ||| ||   |||||| | ||| | || || |||| ||| |||||||| |||||       |  |   |   |    | |   |   | | |||| ||||||  || ||| ||||       |   | | ||  || ||  |    |  |||||  ||||
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgt-------caatacata--tatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag

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|162156858|gb|FC332804.1|FC332804
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|100438193|gb|BY961700.1|BY961700
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|208367351|gb|DC939867.1|DC939867
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|208350568|gb|DC910373.1|DC910373
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|208363544|gb|DC939749.1|DC939749
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|100418836|gb|BY975763.1|BY975763
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|100385804|gb|BY950998.1|BY950998
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|162225703|gb|FC401845.1|FC401845
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|162269559|gb|FC445115.1|FC445115
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
EST: gi|18344483|gb|BJ176523.1|BJ176523
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATA-AAGAGAGCACGTTTAATCAAGAAGCTAGCGAAGAT
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAA-AGAGCACGTTTAATCAAGAAGCTAGCGAAGAT
EST: gi|100416003|gb|BY957030.1|BY957030
EST:     AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAG                         ATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC
genomic: AAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttc ... ttattggtagATATATGTGGAGATAGAAAGAGCACGTTTAATCAAGAAGCTAGCGAAGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttgaacagtatccatattgattcatcgttggttttattggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG