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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc...

Basic information

species Physcomitrella patens
transcript PP1S288_43V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctc-tcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc--------
|||  | ||||||||| |||| || || || || |||  |||||||||||| |||||||| || || |||||||| |||||||| ||| | || ||||||||   |     |      |||||| ||  | ||  ||   ||||||     |  |||      ||   || | | |     | ||   |||      ||          
GCTCGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGTCCGTCGGCAAGACCAGCATCATCACCCGCTTCATGTACGACAAGTTCGACAACACCTACCAGgtg-cgttcttc------ttctctatcggtttcgccgtctgctcgcct--ctcttcggggggttggggttggatctgatcgggggccagatccggcggtggcgccctgg

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgta--atgaatcacaacaaattctctctctctctctcg-ctcgctcgctcggttgctcgct-ctcctgtctttcgttgttccttgtgggtggattgaaaagttc
|||  | ||||||||| | ||||| || || || |||  |||||||||||| |||||||| || || |||||||| |||||||| ||  | || |||||||||  | |   | || |   | || |||||  |||    | || ||| ||  | ||  |||  || |||| |        | ||| ||| || ||     |   
GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggcccgcaccgcctcct-tctctggctccgatcccgatcgatccctcgcgtgctgttcgtgtcatctcccccgcgttgggggcgggttagtggg---

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA01G41090.1 (Glycine max), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaat-tctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc--
 ||| | ||||||||| |||| ||  | |||||||||   || || || ||||||||||| ||||| |||||||||||||| |||||| | || || |||||     |||| | | | | ||||   | || | |   |  |    |   |   | | ||       |    |     |   ||  || | ||  ||      
TCTTGCAAAGTACAAGCTGGTGTTCTTGGGTGATCAGTCTGTGGGAAAAACTAGCATCATCACTCGCTTCATGTATGACAAATTTGACAACACTTATCAGgt--ctgatcagatccactatctcagccactttttaagtttcaatgtgtttcctttgatcagggaaataaaatgacgacaaatgc-tgcactgctaaccatta

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA11G38110.1 (Glycine max), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctc-tcctgtctttcg-ttgttccttgtgggtggattgaaaagttc
 ||  | || |||||| | || ||  | || |||||    |||||||| || |||||||| ||||| |||||||||||||| || |||   |  || |||||  | | |    ||  ||   || | ||| | ||  |       |   |   |||    |   ||    || || |   ||     | || | |     | 
TCTCGCCAAATACAAGCTCGTTTTCTTAGGCGATCAATCGGTCGGCAAAACCAGCATCATCACTCGCTTCATGTATGACAAATTCGACACTAACTATCAGgtctttatttt--accgatctcctttttctttttcttttttatttttaatcattcgaagatttcgttgaacgattatcaatttcaatttgactaactccatt

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA18G02040.1 (Glycine max), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatc-acaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc--
 ||  | || |||||| | || ||  | || |||||    |||||||| || |||||||| ||||| |||||||||||||| || |||   |  || |||||  | | |  |     |    ||||||| | | |  ||||     |    |  ||   |     | |    |  |   || |   |   ||||  | |||  
TCTCGCCAAATACAAGCTCGTTTTCTTAGGCGATCAATCGGTCGGCAAAACCAGCATCATCACTCGCTTCATGTATGACAAATTCGACATTAATTATCAGgtctttattttattcttaccgatctctctttttttttctcgtaattttttgttatcatccgaagatttcctttgatcgattatcaat---ttgactaattcca

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc-----
 ||  | ||||| ||| |||| ||||| || |||||   ||||||||| || || |||||||||||||||||||| ||||| || ||| | || ||||||||||     ||      |           | |||||      | |   |  | | |||   || | ||  |   ||      |||   ||   |  |||      
ACTCGCTAAGTATAAGCTGGTGTTTCTGGGAGATCAATCCGTCGGCAAAACCAGTATCATTACTCGATTCATGTACGACAAATTCGACAACACTTACCAGgtaaatttccattgttcaaatctaggtattatctcgacgatgcac---gacgtttgctt--ctattttgagggattatagtcgggaaaatcccagggtttgattg

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc--
 ||  | ||||||||| | |||||  | || || ||   |||||| |||||||||||||| |||||||||||||| ||||| || ||| | || || ||||| |  ||||   |   ||   ||   |         ||      |  |||| |   | |  ||  ||| ||| |     |    ||  |      | ||  
TCTCGCCAAGTACAAGCTCGTCTTCTTGGGAGACCAATCCGTCGGAAAGACTAGCATCATCACTCGATTCATGTACGACAAATTCGACAACACCTATCAGgtca--aatctttatggatctgcttgtttatcgattttcagcaattttgttggtttgtgttttggttttagttttggtgcgaatttgtttgatcccgatcct

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 2
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcg-ctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc
                   ||||| || || || |||   || ||||||||   |||||| || |||||||||||||||||||| ||  | |||||||||||    | ||    ||  | || |    |     |||  | |  |||     | || |  | | |                                    
-------------------GTCTTCCTGGGAGACCAGTCTGTGGGCAAGACCTCCATCATCACCCGATTCATGTATGACAAGTTCGATAACACGTACCAGgtgcgtactctgcgcatttcctttacaacgacaacgcctgacatgcttttgcggtctccgtgcag------------------------------------

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc
|||| | ||||||||| | |||||||| || ||||||   || || ||||| |||||||| || |||||||||||||| ||||||||| | || |||||||||    || ||    | ||   |||||||| ||       | |     |||     | ||  |                                    
GCTTGCAAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagattac---gagtttcttctctctcact-------ttggcaaattggaaattttcaag------------------------------------

upper sequence: PP1S288_43V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 1
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc
|||| ||||||||||| | |||||||| || ||||||   || || ||||| |||||||| || |||||||||||||| ||||||||| | || |||||||||    || ||    | ||   |||||| || | ||    | |     ||  ||                                             
GCTTGCGAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgtatgagattac---gagtttcttctctcactttggcaaattgg---aatttttcaag------------------------------------------

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|208364171|gb|DC943427.1|DC943427
EST:     CTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAG                         CCAACTATTGGAATTGACTTCCTTTCCAAAACGATGTATTTGGAGGACCGC
genomic: CTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatc ... tgtttttcagCCAACTATTGGAATTGACTTCCTTTCCAAAACGATGTATTTGGAGGACCGC
EST: gi|100399579|gb|BY972789.1|BY972789
EST:     CTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAG                         CCAACTATTGGAATTGACTTCCTTTCCAAAACGATGTATTTGGAGGACCGC
genomic: CTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatc ... tgtttttcagCCAACTATTGGAATTGACTTCCTTTCCAAAACGATGTATTTGGAGGACCGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTCGAAGTACAAGTTGGTCTTTCTTGGTGATCAGAGCGTCGGCAAGACTAGCATCATTACTCGATTCATGTATGACAAGTTTGACCAGACGTACCAGgtaatgaatcacaacaaattctctctctctctctcgctcgctcgctcggttgctcgctctcctgtctttcgttgttccttgtgggtggattgaaaagttc

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