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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatgctggtctagtaaatcagatatcttagtttccatcatgggtgcgatatcgagacaatggctttggtaatcgttgctcactgtaggctagtt...

Basic information

species Physcomitrella patens
transcript PP1S145_164V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S145_164V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g21260.1 (Oryza sativa), 5'ss of exon 2
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatgctggtctagtaaatcagatatcttagtttccat-catgggtgcgatatcgagacaatggctttggtaatcgttgctcactgtaggctagtt---
| || || ||  | ||||| ||||| |||||||| || |||||||| ||||||||||||||||| || ||  | || |||||||  || | |   || |||||    || || || |       |   |   || |     |  |||        | | |||    |   ||   ||     |    | | |    |       
AGGCTCACGGGACGGCGGTGGGGCTGCCTACGGACGACGACATGGGCAACAGTGAGGTTGGCCACAACGCGCTTGGAGCAGGCCAGATATATGCCCAGGGgta----atactagttttagggcccctttgaattggaggaaaaacatataaaaattttagaggattttaattctataggaaatatagaatttcctatgaagccc

upper sequence: PP1S145_164V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 5'ss of exon 3
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatgctggtctagtaaatcagatatcttagt-ttccatcatgggtgcgatatcga--gacaatggctttggtaatcgttgctcactgtaggctagtt
| || |||||| | || || || || ||| | || || ||||||||||||||||||||||| ||||| ||  | ||||| || || ||||||   ||||||||   |||| |  ||  |    ||   | | ||||    |  |||    |    | | ||  | |||    | | |   | ||| || |  ||    |    
AGGCTCATGGAACAGCTGTTGGTCTCCCTTCTGATGATGACATGGGTAACAGTGAGGTTGGGCATAACGCACTTGGTGCTGGTCGGATTTTTGCTCAAGGgta---catgtttctcctggttctcttttttattagcacactgtcagttataatctgtggatggccaaaaagtattgcgtttgtttctaaaggtcttattaca

upper sequence: PP1S145_164V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 2
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgta----tgtcatgctggtctagtaaatcagat-atcttagtttccatcatgggtgcgatatcgagacaatggct-ttggtaatcgttgctcactgtaggctagtt
| || |||||   ||| |||||||| || || ||||| |||||||| |||||||| ||||||||||||||| | ||||| || ||||| | |   |||||||     | || | ||| | |  |   |   || |  ||  |    || ||       |||     |  ||| |  ||   ||   |   ||  | | |       
AGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTCTTGGTGCTGGACGCATATATGCTCAAGGgtgaatttctcttcctgattttatttcttttatgaaatttttacatattataacctttatacacccaggatgtcccttcacaagtttgattcctttttga------

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|162243941|gb|FC424285.1|FC424285
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
EST: gi|100361375|gb|BY965809.1|BY965809
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
EST: gi|100441305|gb|BY962594.1|BY962594
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
EST: gi|100363611|gb|BY966473.1|BY966473
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
EST: gi|162185692|gb|FC362066.1|FC362066
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
EST: gi|100397615|gb|BY990315.1|BY990315
EST:     AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGG                         TGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA
genomic: AGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatg ... atctgttcagTGCAAGCCTCGTTGATACTTCTCTCGAGTCTGGTGCGATATATGAAGGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCCCATGGAGCTGCGGTAGGGCTACCTACGGAGGAGGACATGGGTAACAGTGAGGTTGGCCATAATGCTTTGGGTGCAGGCCGCATTTTTAAGCAAGGgtatgtcatgctggtctagtaaatcagatatcttagtttccatcatgggtgcgatatcgagacaatggctttggtaatcgttgctcactgtaggctagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG