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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCATTCCAAGGACTTCGTAGTCGGGGGCACTGCGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccattattctagttcatgttacgagtcctgttttttttttttctctcag

Basic information

species Selaginella moellendorffii
transcript EFJ32896
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32896 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G045371_T02 (Zea mays), 5'ss of exon 5
CGAGCATTCCAAGGACTTCGTAGTCGGGGGCACTGCGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatt---attctagtt-----catgttac---gagtcctgttttttttttttctctcag-------------------------------------------------------------------------------------------------
 ||||   ||||||| || || ||    || || || || ||||| |||||||||||||| || || ||||||||||| |||||||||  |  |   || |  | |     | | || |   |||  |   |||| ||||   |||  |                                                                                                 
GGAGCTGGCCAAGGATTTTGTTGTTTCTGGAACAGCATCAGAATCTTTGTATGGTGCTTGTGAATCCATGTACAAGCCGGACATGgtatgcgcttcgatgcatgctgtcgacctatttccttgagatccacttttgttttgggtctgcgtatacccatgttttatgatctatttttggatgtacattattgtagtttgttctgtttttagttgaatgacatcatcttgttatttttcatggcatag

upper sequence: EFJ32896 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G092975_T01 (Zea mays), 5'ss of exon 5
CGAGCATTCCAAGGACTTCGTAGTCGGGGGCACTGCGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccattattctagttcatgttacgagtcctgttttttt--------tttttctctcag-------------------------------------------------------------------------------------------------------
 ||||   ||||||| || || ||    || || || || ||||| |||||||||||||| ||||| |||||||||||  ||||||||  |  |       | ||||||  ||  ||| |||   |         |||| | |  |                                                                                                       
GGAGCTGGCCAAGGATTTTGTTGTATCTGGGACAGCATCAGAATCTTTGTATGGTGCTTGTGAGTCCATGTACAAGCCGAACATGgtatgcgct---tcgatgcatgttgtgaa-cctatttccctgagatccacttttgttttgggtctgcgtctaccatgttttatgaagttctaatttggggtgtacattactgtactttgttctattcttagtcaaatgacatcttgttatttttcatgacatag

upper sequence: EFJ32896 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S130_217V6.1 (Physcomitrella patens), 5'ss of exon 6
CGAGCATTCCAAGGACTTCGTAGTCGGGGGCACTGCGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccattattctagttcatgttacgagtcctgttttttttttttctctcag-----------------------------------------------
  | |   | ||||||||||| ||    || ||||| || || ||| ||||||||||||||||||||||||| || || ||  |||||    |  ||||         | |   || | |   || || ||                                                      
GCAACTGGCGAAGGACTTCGTGGTTTCTGGAACTGCCTCAGAGTCCCTGTATGGTGCTTGCGAGTCTATGTATAAACCTGATTTGgtatgtttagttctttgcaccaatgcctatcgtatacgttcttattaaaatgtggggtttattttcatgtccttctgaatataaggcctctttagcgttg

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|169049745|gb|FE457785.1|FE457785
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169101740|gb|FE501245.1|FE501245
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169045729|gb|FE451702.1|FE451702
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169043818|gb|FE453809.1|FE453809
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169049744|gb|FE457784.1|FE457784
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169069806|gb|FE480305.1|FE480305
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|70669820|gb|DN838397.1|DN838397
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169045728|gb|FE451701.1|FE451701
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
EST: gi|169043817|gb|FE453808.1|FE453808
EST:     CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATG                         GAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT
genomic: CGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTT

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: 32 (upstream exon), 35 (downstream exon)
Score: 54

CGAGCATTCCAAGGACTTCGTAGTCGGGGGCACTGCGTCTGAATCCTTGTATGGTGCTTGCGAGTCTATGTACAAGCCCGACATGgtaaccatta ... tttctctcagGAGCCTGAAGACCTTTTTGAAACGATCTCACAAGCGCTGATCTCCTCGGTTGATCGTGACTGTCTGAGCGGCTGGGGAGGAATCGTCTACGTTGT




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