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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgggatcttgaatttattctgaattattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacctgcctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG

Basic information

species Physcomitrella patens
transcript PP1S120_29V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 1
gttcgggatcttgaatttattctgaattattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacc-tgcctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
     | ||||||    |        ||      |||   | |    |  |   ||  |  ||| ||        || | ||| |     |   |  ||| | ||  |      ||||||| || ||| |||| |||||||||||||| |||||||| ||| |  | ||||| ||||||||  |||||||||| |||||||| || |||||||||    
-----gaatcttgtgcctgc----ggttgcca--tttgcctggaagaacctgaaatt-ttgttccagtcct----atttttccttataaattttggttccctaactgttatagtacAAGACAAATGTGATGGGGACCTTGAACATGCTGGGATTGGCAAAGAGGGTGGGAGCCCGGTTCTTATTGACCAGTACCAGTGAGGTGTACGGTGATCCTC---

upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
gttcgggatcttgaatttattctgaattattgagtttatgtagtgt-tattttgcatagtccttctagcagagagaatgtatccgtggtcgtgca---gcctccttgacctgcc-tccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
                       | | | ||| | ||  || | |  ||   || ||   | |      |    |  ||| |   |  |  | ||   |  || || |||  |  |  ||||||| || ||  |||| |||||||| ||||||||| |||| ||| |  | || || ||||||||| |||| ||||| ||||| || |||||||||||| | |
-----------------------gtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG

upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G347717_T03 (Zea mays), 3'ss of exon 1
gttcgggatcttgaatttattctgaattattgagtttatgtagtgt-tattttgcatagtccttctagcagagagaatgtatccgtggtcgtgca---gcctccttgacctgcc-tccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
                    | || | | ||| | ||  || | |  ||   || ||   | |      |    |  ||| |   |  |  | ||   |  || || |||  |  |  ||||||| || ||  |||| |||||||| ||||||||| |||| ||| |  | || || ||||||||| |||| ||||| ||||| || ||||||||||||    
--------------------tttgtagttttgtgcttgcgtggggaatagcctgtatttacatctgtttattttgtctgtttttttttttcttcaattgtttctttaaccaactatgtacAAGACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTC---

upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ30517 (Selaginella moellendorffii), 3'ss of exon 2
gttcgggatcttgaatttattctgaattattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacct-----gcctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
  ||  ||    ||   ||| ||    | |    |||   |  | ||  ||||  | |  | |||| |        | | |   |  |  ||  || ||||| ||       || | ||||||||||||||||| |||||  | |||||||| |||||||| ||||| || || || ||||| ||||||||||| || || ||||||||||| |||||  |||
-gtcaagac---gatcatatcct----tttcttctttgcttgttcttcgtttgtttcgagcatctaacgcgtgt--tttttttttttttttgttgcttccttaactcttggagctttcacaagACCAACGTGGTTGGAACACTCAACATGCTCGGATTGGCCAAGCGAATTGGTGCTCGGTTTTTGCTGACCAGCACAAGCGAGGTTTATGGAGATCCGCTGG

upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ23020 (Selaginella moellendorffii), 3'ss of exon 1
gttcgggatcttgaatttattctgaattattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacct-----gcctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
               |  |  |     |||    ||  | |    || || | | |  || ||| ||||   |    || |   |  ||||   || ||||| ||       || | ||||||||||||||||| |||||  | |||||||| |||||||| ||||| ||||| || ||||| ||||||||||| || || ||||||||||| |||||  |||
--------------gtcaagacgatcatatccttttcttctttgcttgttcttcgtt-tctttcgagcatctaacgcgttttttttttcgt--tgcttccttaactcttggagctttcacaagACCAACGTGGTTGGAACACTCAACATGCTCGGATTGGCCAAGCGAATCGGTGCTCGGTTTTTGCTGACCAGCACAAGCGAGGTTTATGGAGATCCGCTGG

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|162239441|gb|FC414032.1|FC414032
EST:     CGCCCGTGCATTACAAATTCAATCCAATCAAGACTATCA-A--------G                         ACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGA
genomic: CGCCCGTGCATTACAAATTCAATCCAATCAAGACTATCATATCCTTTTTTgttcgggatc ... cctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcagagagaatgtatccgtggtcgtgcagcctccttgacctgcctccacaagACCAACGTGGTGGGAACCTTGAACATGCTTGGATTGGCGAAGCGCATCGGAGCACGGTTCTTGCTGACCAGTACTAGTGAGGTTTATGGTGATCCTTTGG
                                   ccttgac  putative branch site (score: 4)
                                         cctgcctcc  CT-rich tract
           aatgtat  TA-rich tract