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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttccttcttgaccttagtattcattttatcttagtaatctattgatctattttcctgatgctgaatttcataagcttgaatacag

Basic information

species Physcomitrella patens
transcript PP1S46_63V6.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 5'ss of exon 9
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttc----cttcttgaccttagtattcattttatcttagtaatctattgatctattttcctgatgctgaatttcataagcttgaatacag
||| ||  | ||  ||   |||||    || || ||||| || ||||||||||| ||||| ||||| || ||||||||||| || || ||||||||||||||||||      ||  |     | |||| |   | | | | |  | | | || |  |  |   ||||   | |  || ||  ||   |      
TGAAGCCCTGAAACAAGGAAAGGTTCAGAAACCTGTTGTTGCATGGGTTAGTGGGACATGCGCTCGTCTATTCAAGTCTGAAGTGCAGTTTGGCCATGCTgtaagtctgaaactgttccttttcagtaatttctgtgt-tgaacagtattttaag-tgctcatctga-attaa--tttattggcccaacag---

upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G002416_T01 (Zea mays), 5'ss of exon 4
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttccttcttgac-cttagtattcattttatcttagtaatctatt----gatctattttcctgatgctgaatttcataagcttgaatacag---
 || || || ||  ||   ||||||   || |||||||| || ||||||||||| |||||||| || || ||||| || || || || ||||||||||||||||||            |||    | ||||    | | |   ||| |     || |  | |   |  |    |      |    | | | | |    
GGAAGCATTGAAACAAGGAAAGGTCCAGAAACCAGTTGTTGCATGGGTTAGTGGGACATGTGCACGTCTATTCAAATCAGAAGTGCAGTTTGGCCATGCTgtaagtattagaagattacttgaactccattcccccctgggtttctgtcagaagaacagtatatttactatccagagatctttcttgggacataacag

upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA15G15020.1 (Glycine max), 5'ss of exon 9
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttc---cttcttgaccttagtattcattttatcttag----taatctattgat---ctattttcctgatgctgaatttcataagcttgaatacag
 || || |||||  ||   |||||   ||| || ||||| || ||||| |||||||||||||| ||||| ||||| ||||| || |||||||| ||||| ||| ||     || ||| | ||| |  |  ||| |   |||     ||| | ||  |    | |  ||| | |||     |  |    || | ||| |||
GGAGGCCTTAAAACAAGGAAAGGTATCCAAACCGGTTGTTGCCTGGGTCAGTGGCACATGTGCACGACTCTTCAAATCTGAAGTACAATTTGGTCATGCAgtatgtctcagctcctttaactttgactaaattctcaattaaagcataaaccataaaaggacaacattcttaatgtctgttggctcttgcataaat-cag

upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA07G36840.1 (Glycine max), 5'ss of exon 10
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttcctt-cttgaccttagt-attcatttt--atcttagtaatc-tatt----gatctattttcctgatgctgaatttcataagcttgaatacag
 || ||  ||||  ||  ||| || |  || ||||| || ||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||||||| ||  ||  |   |  ||  | | | ||| |   |  ||| | |  || |    || | |  ||||||||| | | |  ||   |  | |||  ||
GGAAGCCCTAAAACAAGGGAAAGTGACTAAACCAGTGGTTGCTTGGGTTAGCGGAACCTGTGCACGACTCTTCAAATCTGAAGTACAATTTGGTCATGCTgtatgtcactggcccaatatttttgactaattctcagttatagcatttataataagggagccaaattcctgatgttcattggcacttgtataaat-tag

upper sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 9
TGATGCTTTAAAGGAAAAGAAGGTCAGCAAGCCAGTTGTGGCTTGGGTTAGTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttccttctt-gaccttagtattcattttatcttagtaatctattgatctatttt--cctgatgctgaatttcataagcttgaatacag
||| ||||| || ||    || ||||  || || || || |||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| ||||||  |      || |||   |  || |   | ||  | |||| |||  | | |       | |  ||||  |  ||    ||||||   
TGAAGCTTTGAAAGAGGGAAAAGTCAATAAACCTGTGGTTGCTTGGGTCAGTGGAACTTGTGCACGACTCTTCAAGTCTGAAGTACAGTTTGGTCATGCAgtaagtggcgcggaagaactttcaaagcaatgccttttttttatctcttgtacaaatcaaaatagttcttgaacatgttatatatgaatag--

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|67574889|gb|BJ947713.1|BJ947713
EST:     GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCT                         GGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
genomic: GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttcct ... ttgaatacagGGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
EST: gi|162197631|gb|FC374465.1|FC374465
EST:     GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCT                         GGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
genomic: GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttcct ... ttgaatacagGGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
EST: gi|162150458|gb|FC326106.1|FC326106
EST:     GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCT                         GGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
genomic: GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttcct ... ttgaatacagGGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
EST: gi|162196012|gb|FC372183.1|FC372183
EST:     GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCT                         GGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
genomic: GTGGCACATGTGCTCGACTTTTCAAGTCTGAGGTTCAATTTGGCCATGCTgtaagttcct ... ttgaatacagGGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
EST: gi|100385297|gb|BY950889.1|BY950889
EST:     CAATTTGGCCATGCT                         GGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT
genomic: CAATTTGGCCATGCTgtaagttcct ... ttgaatacagGGCGCAAAGAGTGGTGGAGATGAGGAGTCTGCTCAAGCCAAAAACAAAGCT