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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttgatgacatttcgtgttctaattttcctaaatgcatttaagtgttcccacatttgcatgaactaaaccctacaagtccgt...

Basic information

species Physcomitrella patens
transcript PP1S385_43V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 7
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttga-tgacatttcgtgttctaattttcctaaatgcatttaagtgtt--cccacatt--tgcatgaactaaac-cctacaagtccgt---------------------
 | || ||||| || ||   ||| || ||||||||||| || ||||| || || ||||||||||| || || || || ||||||||||||||||     || |  ||||| | ||  ||  ||    ||||       || | |     | ||     ||| |  ||   |  | |||  |  | | ||  ||                     
CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcag

upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 6
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttgatgacatttcgtgttc-taattttcctaaatgcatttaagtgttcccacatttgcatgaactaaaccctacaagtccgt----------------------------
 | || |||||||| ||  |||| || ||||||||||| ||||| ||||||||||||||||||||  | || || || |||||||||||| ||||||    ||   ||  |  | ||  ||  |  | ||   | | ||     |   |       | | || | ||| |    ||   ||  ||| |                            
CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCACTTGGGGAGTTCATACTAACCCATCCAGACATCAAGgtt-atatcttctcgtagcttctt--cgttcagtccttgtcatgcacgtgaagttgctcgggcaacagaatacttac-tgatcactgccactcatctccctctttgcattgtgacgcgcgcgcgcgcag

upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G322953_T03 (Zea mays), 5'ss of exon 5
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttgatgacatttcgtgttctaattttcctaaatgcatt-taagtgttcc----cacatttgcatgaactaaaccctacaagtccgt-------------------------------
 | || |||||||| ||    || || ||||||||||| ||||||||||| ||||| |||||||| ||||| || ||  | ||||||||| ||      |    ||         |||  | | ||   |   | | |  | |  | ||   |      || | | | |  |  | |        |   |||                               
CTTGTGCTGAGCACTGGGAACGGAGTCAATGGCTTCACTCTCGATCCTTCCCTTGGAGAGTTCATTTTGACTCATCCAAATATCAAGgttaatgataaaaaaaactccacacttcttttctttcctggctgatcgatacccctggttagcactataaaacaaaatggtactacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcag

upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA20G30620.3 (Glycine max), 5'ss of exon 7
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttgatgacatttcgtgttctaattttcctaaatgcatttaagtgttcccacatttgcatgaactaaaccc-tacaagtccgt
 | ||  | ||||| ||   ||| |||||||| |||||||| ||||| || ||||||||||||||  | || ||||||||||||||||| |  |||||   ||| ||    |  | ||  | ||||   | |      |    |     |   | ||  ||  |  |   | |    | |||      
CTTGTGTTAAGCACTGGAAGTGGTGTTAATGGTTTCACCCTTGATCCATCTCTTGGGGAGTTCATTCTAACTCACCCTGACATCAAGgtattaatctgcccgtcgttcatagtaaattgttattctctctgtaaatgctctggtctgacgactcaactcttaaaaaagtcacatttgttcaaactaa-

upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA10G36990.2 (Glycine max), 5'ss of exon 7
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatctgtatgtcctttgatgacatttcgt-gttctaattttcctaaatgcattta---agtgttcccacatttgcatgaactaaaccctacaagtccgt
 | ||  | ||||| ||   ||| |||||||| |||||||| ||||| || |||||||| |||||  | || ||||||||||||||||| | |||   | |  || | | | | | |   | ||| |  | |   |||||||  |      | |     ||| ||  |  |   | |   |   |  |   
CTTGTGTTAAGCACTGGAAGTGGTGTTAATGGTTTCACCCTTGATCCATCTCTTGGGGAATTCATTCTAACTCACCCTGACATCAAGgtat-tattaatctacccatcgttcatagtaaattgttattctctctgtaaatgctctggcctggcgacttaacagttaaaaaagtcacattttttcaaac---

upper sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGg-----tttat-atctgtatgtcctt-tgatgacatttcgtgttctaattttcctaaatgcatttaagtgttcccacatttgcatgaactaaaccctacaagtccgt
 | ||  | ||||| ||  |||| |||||||| || ||||| ||||| |||||||||||||||||  | || |||||  |||| ||||     ||||| || ||  ||||      || |||||     | ||  ||| |   |||   ||      || |     |   | | |  | |      ||      
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatcacatta-acatgctgttttcctctaatattttccctacttgctgacatcttaaggaggatatgtgggaa------

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|162247228|gb|FC423052.1|FC423052
EST:     CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
genomic: CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|162247229|gb|FC423053.1|FC423053
EST:     CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
genomic: CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|100385375|gb|BY950967.1|BY950967
EST:     CCTCGATCCTTCACTTTGGGGAGT-CATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAAATTACTCTGTNAACGAAGGAAATGCCAAACAC
genomic: CCTCGATCCTTCACTT-GGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|37843043|gb|BJ601051.1|BJ601051
EST:     CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
genomic: CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|100390324|gb|BY952732.1|BY952732
EST:     CCTCGATCCTTCACTTGGGGGAGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAATTTACTCTGTTTACGAAGGAAATGC-AAACAC
genomic: CCTCGATCCTTCACTTGGGG-AGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|100352580|gb|BY945343.1|BY945343
EST:     CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAGGAAGGGAAAAATTTACTCTGTTAACGA-GGAAATGCCAAACAC
genomic: CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
EST: gi|100411169|gb|BY992231.1|BY992231
EST:     CCCTCGATCCTTCACTTGGGGGGTTCATCTTGACGCACCCTGACATCAAG                         ATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC
genomic: CCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 8

TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGgtttatatct ... atttcatcagATTCCTAAGAAGGGAAAAATTTACTCTGTTAACGAAGGAAATGCCAAACACTGGGACGGTCCTACAACCAAGTATGTGGAGAACGCAAAGTTCCCCAAGG




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