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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttggttgaaagtatttggtatgagtttgagtatgttaactaatcctggatcactttcgagtattcaagaaattaaaattggtcatgtctcttg...

Basic information

species Physcomitrella patens
transcript PP1S381_39V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA09G29970.1 (Glycine max), 5'ss of exon 6
GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaag--ttttggttgaaagtatttggtatgagttt-gagtatgttaactaatcctggatcactttcgag-tattcaagaaattaaaattggtcatgtctcttg
| | || ||  | || || || || | ||   |  |   ||||||||||||  |  | |||| |||||| ||||| |||| ||| ||||||||||||||||||||  ||||  ||  ||   ||||    | |||  ||     ||  ||||  | |     |      | | |  ||    ||||||||  | |    |  | 
GATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACATATAAGTACTTCACAAAAAATCATATGCTTTATGAACGGAATCAGgtaagaattttatttctaa---tttgaggagtgttaagaacgcattccctaacacagtccttccaatacgctctctaattggttaaaatttattaaaaattat-

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA08G06160.1 (Glycine max), 5'ss of exon 8
GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagt-tttggttgaaagtatttggtatgagtttgagtatgttaactaatcctggatcactttcgagtattcaagaaattaaaattggtcatgtctcttg---
| | || ||  | ||||| || || | | |  |  |    |||||||||||| |  | |||| |||||||||||| || | ||| |||||| |||||||||||||  |||  |    |   ||  |||  |  | || || |   |  |||   | ||   ||     |  | |   | ||   |   | || | || ||    
GATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACATATAAGTACTTCACCAAAAATCACATGCTTTATGAAAGGAATCAGgtaagaattttatatctaaccttgtgtaccaactggactaggc--atgaatttggaatg--ttgatgttgattagctagttcctaggagccagggcttttatgt

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA16G34510.1 (Glycine max), 5'ss of exon 6
GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagt-tttggttgaaagtatttggtatgagtttgagtatgttaactaatcctggatcactttcgagtattcaagaaat--taaaattggtcatgtctcttg
| | || ||  | || || || || | ||   |  |   ||||| ||||||  |  |||||| |||||| ||||| |||| ||| |||||||| |||||||||||  |||  ||   | | |  ||  ||   || || |      |||   |    ||  |       | |||  || |  | |||||  | |    |  | 
GATTGGTATAATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGCACGGGATACATACAAGTACTTCACAAAAAATCATATGCTTTATGAACGAAATCAGgtaagaattttatttttaatttgaggagtg---ttaagaacacattctataacatagtccttcaaatacactcactaattggttaaatttattaaaaattata

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 5'ss of exon 12
GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttggttgaaagtatttggtatgagtttgagtatgttaact----aatcctggatcactttcgagtattc-aagaaattaaaattggtcatgtctcttg
| | |||||  ||||| | || |||| ||   |  |   ||||||||| ||  |  | || |  ||||||||||| || | |||||||||||||||||||||||   ||  ||      || ||  |  | | |   | | || |||    ||  |    |   || | | | | | | | | ||     |  |||||       
GATTGGAATAATAGGTTCAATTGACCAAGGCATGCTTGCTAAAGGACGTGATACATATAAATATTTCACCAAAAATCACATGCTCTATGAACGGAATCAGgtaacagtttattttcctcatctgtaagaactctt--tctcttgacttttaaaatccaagtaggttgccattctcctatgtatttggtgataatcatgctca---

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|162271795|gb|FC448928.1|FC448928
EST:     ACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAG                         GATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT
genomic: ACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttg ... tggttggcagGATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT
EST: gi|162271794|gb|FC448927.1|FC448927
EST:     CACCAAAAACCATACGCTCTATGAACGGAATCAG                         GATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT
genomic: CACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttg ... tggttggcagGATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT
EST: gi|162242877|gb|FC415307.1|FC415307
EST:     ACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAG                         GATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT
genomic: ACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttg ... tggttggcagGATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCAT

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: 16 (upstream exon), 32 (downstream exon)
Score: 2

GGTAGGAATTCTAGGTCCTATCGACCCAGAGCTTTTAAGTAAAGGACGGGACTCTCACAAGTTCTTCACCAAAAACCATACGCTCTATGAACGGAATCAGgtaagttttg ... tggttggcagGATTCTGACCAACTGGAGTATCTGCTGCCAAAGAAAACATCTCTGGCCCATCGGCTACCCATGGGCGACCAGGGCTTTGTGGCATTTGTTGGCTACCTTC




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