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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTGCAGAAGCATGGAAATCCTGACATTGTAATGGCTTTGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctctgtctttgtgaaatgacgtcttctttagcagcaatcgtggcacattgtgtggtgtgtaattcagctgtggatggactaaatgagatacttggcgtctgaagtgtattccgttgactctgtag

Basic information

species Physcomitrella patens
transcript PP1S38_328V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S38_328V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 7
GAGCTGCAGAAGCATGGAAATCCTGACATTGTAATGGCTTTGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGT-TACTCGCGAGgtaagttctctg-tctttgtgaaatgacgtcttctttagcagcaatcgtggcacattgtgtggtgtgtaattcagctgtggatggactaaatgagatacttggcgtctgaagtgtattccgttgactctgtag
|| || ||||||||||| | |||||  |||||||||| ||||||||| ||||| ||||| ||  |  || | ||    || | |||||  |  |   | | || ||||||  || |||    |  | |||    ||| |  ||  | | | || |       |   |  |  |||||    |||   ||||||  |                            
GAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtatatgctctttgccaactgatagatattgtagt--taatggctgc-tactatatgat------cttgaccat--atggat---atggtgtacttgttgcag-------------------------

upper sequence: PP1S38_328V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G362088_T01 (Zea mays), 5'ss of exon 6
----------GAGCTGCAGAAGCATGGAAATCCTGACATTGTAATGGCTTTGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGT-TACTCGCGAGgtaagttctctg-tctttgtgaaatgacgtcttctttagcagcaatcgtggcacattgtgtggtgtgtaattcagctgtggatggactaaatgagatacttggcgtctgaagtgtattccgttgactctgtag
          || || ||||||||||| | |||||  |||||||||| ||||||||| ||||| ||||| ||  |  || | ||    || | |||||  |  |   | | || ||||||  || |||    |  | |||    ||| |  ||  | | | || |       |   |  |  |||||    |||   ||||||  |                            
CATTCCACAGGAACTTCAGAAGCATGGTAGTCCTGGTATTGTAATGGTTTTGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtatatgctctttgccaactgatagatattgtagt--taatggctgc-tactatatgat------cttgaccat--atggat---atggtgtacttgttgcag-------------------------
















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|162267081|gb|FC443312.1|FC443312
EST:     TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAG                         GAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
genomic: TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctc ... gactctgtagGAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
EST: gi|162276874|gb|FC452556.1|FC452556
EST:     TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAG                         GAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
genomic: TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctc ... gactctgtagGAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
EST: gi|7648245|gb|AW739228.1|AW739228
EST:     TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAG                         GAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCT
genomic: TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctc ... gactctgtagGAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
EST: gi|162152195|gb|FC328174.1|FC328174
EST:     TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAG                         GAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG
genomic: TGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctc ... gactctgtagGAAGCACAGACATATGCCGATAGTAATGGCATGTTCTACATCGAAACGTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTGCAGAAGCATGGAAATCCTGACATTGTAATGGCTTTGGTTGGCAATAAAGCTGACCTCGAATATCAACGTGAAGTTACTCGCGAGgtaagttctctgtctttgtgaaatgacgtcttctttagcagcaatcgtggcacattgtgtggtgtgtaattcagctgtggatggactaaatgagatacttggcgtctgaagtgtattccgttgactctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA