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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctcaccttcagtgcttgttacaacacgagtctgcattggcggagcagtataaatatctctctgggttttccccttcaggaatctgcttagagagctagcctctatttcgtttgcaaatcatgagcttctgcaagttcacttcagtattttaatgaattttttagactttcttaacagtttctgtatctggcag

Basic information

species Physcomitrella patens
transcript PP1S35_209V6.1
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_209V6.1 (Physcomitrella patens), 5'ss of exon 28
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 28
AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgt-aggcctcaccttcagtgcttgttacaacacgagtctgcattggcggagcagtataaatatctctctgggttttccccttcaggaatctgcttagagagctagcctctatttcgtttgcaaatcatgagcttctgcaagttcacttcagtattttaatgaattttttagactttcttaacagtttctgtatctggcag
| |||||| | ||   |||||| ||||||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| | | |||| |  || ||||||| |||| |||  ||| || ||      |||||   | | |  |||   | |     | |  | |  ||| | | ||  |||      |||  |||   ||  |  | | |  ||                                                                                     
ATCACAAACCCAAGGGCGATGCAGTGAAGCAAGAGGTTGATCGCAATGAAGACATGATTCGAAGTGCTCTTCGAGCAATCGCTGCTCTAAGCCGCATAAGgtcaggcatca--ttctgtcctgccccgaacactttttttc--tggtttaac----cacacttttaactgtgctgtcatctt------tctcgttatt-agtgaatcgccacatc-------------------------------------------------------------------------------------

upper sequence: PP1S35_209V6.1 (Physcomitrella patens), 5'ss of exon 28
lower sequence: GRMZM2G168629_T01 (Zea mays), 5'ss of exon 28
AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctcaccttcagtgcttgttacaacacgagtctgcattggcggagcagtataaatatctctctgggttttccccttcaggaatctgcttagagagctagcctctatttcgtttgcaaatcatgagcttctgcaagttcacttcagtattttaatgaattttttagactttcttaacagtttctgtatctggcag
  |||||| | ||    ||||| |||||||| |||||||| || || |||||||||||||| ||||||||  | |||||   |||||| |  || ||||||||      | ||| |    | ||| |  | | | |||   ||          ||      ||  |    |||      |||   ||   | ||  |   ||   |  | | |||  | ||  |  |   | | || || | |  | || || | ||||| |                                     
GCCACAAACCCAAGGGGGATGCAGTGAAGCAGGAGGTTGATCGGAACGAGGACATGATCCGCAGCGCTCTCAGGGCAATATCTTCTCTAAGCCGCATAAGgtaaaa---agcttga---ttcgtttc--cgccattctatctt----------taccctcgtcctttaccgttcgattgttcgacaaaaaggttccaaccctttaccatctctcgccttcattttttcgccctatg-aactacgttaca-taatgtaatgcag------------------------------------

upper sequence: PP1S35_209V6.1 (Physcomitrella patens), 5'ss of exon 28
lower sequence: EFJ33911 (Selaginella moellendorffii), 5'ss of exon 26
AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctcaccttcagtgcttgttacaacacga--gtctgcattggcggagcagtataaatatctctctgggttttccccttcaggaatctgcttagagagctagcctctatttcgtttgcaaatcatgagcttctgcaagttcacttcagtattttaatgaattttttagactttcttaacagtttctgtatctggcag
   ||||||||||||| |||||||| || |||||||| || || || || ||||||||||| || || |||||||| |||||||||||| |  | ||||||||       | ||   |   |  |  |    ||  ||||  |||  |                                                                                                                                                         
CCAACAAAACAAAACCGGATGCTGTCAAACAAGAGGTGGATCGAAACGAAGACATGATCCGGAGTGCACTTCGTGCCATTGATTCTCTGGACAGAATAAGgtacatacttctttggttcgcttctggattctgatggtcttgattttccag------------------------------------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S35_209V6.1 (Physcomitrella patens), 5'ss of exon 28
lower sequence: EFJ37421 (Selaginella moellendorffii), 5'ss of exon 26
AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctcaccttcagtgcttgttacaacacgagtctgcattggcggagcagtataaatatctctctgggttttccccttcaggaatctgcttagagagctagcctctatttcgtttgcaaatcatgagcttctgcaagttcacttcagtattttaatgaattttttagactttcttaacagtttctgtatctggcag
   ||||||||||||| |||||||| || |||||||| || || || || ||||||||||| || || |||||||| |||||||||||| |  | ||||||||  | |   |||  || |   |    |  |   |  |  |||      |||                                                                                                                                                  
CCAACAAAACAAAACCGGATGCTGTCAAACAAGAGGTGGATCGAAACGAAGACATGATCCGGAGTGCACTTCGTGCCATTGATTCTCTGGACAGAATAAGgta--catattctttggttcgcttctggattctgatg-gtcttgattttccag--------------------------------------------------------------------------------------------------------------------------------------------------

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|162219608|gb|FC395604.1|FC395604
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
EST: gi|162157670|gb|FC332992.1|FC332992
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
EST: gi|162157669|gb|FC332991.1|FC332991
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
EST: gi|37822150|gb|BJ580216.1|BJ580216
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
EST: gi|162158276|gb|FC334695.1|FC334695
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
EST: gi|162163408|gb|FC339734.1|FC339734
EST:     GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAG                         TGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT
genomic: GACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 32 (downstream exon)
Score: 11

AACACAAAACAAAACCCGATGCTGTGAAGCAAGAGGTTGACCGTAATGAGGACATGATCCGAAGCGCTCTTCGTGCAATTGATTCTCTGAATCGGATAAGgtaggcctca ... tatctggcagTGGGGAGCCTACACCTCGATTCAAGGCTTTCATGAACCATGTGGTCAAGGTAGGTTCGCTTGGAGAGAAATACAACGTGGTGCGTCATGAGAGCGACACT




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