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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccattttattacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct...

Basic information

species Oryza sativa
transcript LOC_Os07g22710.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 6
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccattttattacatgt---gtttcattgattaaaactattttcttgccttacaatcactatattttcttct
 |||||||| || ||||||||||| || || |||||||||||| | ||||||||||||||||| |||||||||||||| |||||||| |||||||||||||| |   | |||||  |||||      |  || |||||| ||||||||    | | ||   |  ||    |||  |||| |  |     |||  |  | ||  
GCCAGAATCCGATGTTTGGAGTATAGGTGTTATAACCTATATTTTGCTGTGTGGAAGACGACCATTCTGGGACAAAACAGAAGATGGGATATTTAAAGAGgttaacat-cctaagttatctcgactctgtaatcatttttttacatgtccaatattatatgtggaagtgctttgtttgcatgtcccatgctaattaatttt--

upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 5'ss of exon 6
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaa-ccattttattacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct
 || ||||| ||||||||||||||||| || || || || ||||| || || || ||| |||| |||||||| || ||| |||| |||||||| || ||||||   | |     |   ||||      |||| ||| | |||   || |||||  || ||  | ||||||  | ||    | || ||              
ACCTGAATCAGACGTTTGGAGTATTGGTGTCATCACTTACATTCTGCTCTGCGGGAGAAGACCCTTCTGGGATAAGACTCAAGACGGAATATTCAATGAGgtc---tagtactcatcttcttgagaaaacaatccaatctatataatctgttt-gttcatggatactattgacatg---aaaaaacag-------------

upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G66210.4 (Arabidopsis thaliana), 5'ss of exon 6
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccattttattacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct
 || ||||| || || ||||| ||||| || || || |||||  |||| ||||| || || ||||| ||||| | |||||||||||| ||||||||||||||    |||   ||||| |||||  ||       ||||   |  ||   |||  ||  ||    ||   ||| |  || | |   |||||||     |  
GCCTGAATCAGATGTATGGAGCATTGGTGTGATTACGTATATATTACTTTGTGGGAGGCGGCCTTTTTGGGATAGAACTGAAGATGGTATATTTAAAGAGgtgtagttga--aaactttctttcactgg-----atttctatctatagcttttcttatttctttctcacttccttactaatatgtactatatgaatatag

upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S83_8V6.1 (Physcomitrella patens), 5'ss of exon 6
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgt---cattttgcctaaact-------atctttgtcttacaaccattttattacatgtgtttcattgattaaa--actattttcttgccttacaatcactatattttcttct--
 || ||||| || || |||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||  | || || || || |||||   ||||  |  |   ||       |  ||   ||| | |   |      |    || | ||||  | |||  || | |   || ||| ||    | |   || |||     
TCCGGAATCAGATGTGTGGAGTATTGGCGTCATTACCTATATTCTGCTGTGTGGGAGGCGACCCTTCTGGGACAAAACTGAGCAGGGGATCTTCAACGAGgtttgcattccgatttttcttcgcgacagtttcagcttgcgagggtacagaaaggattggtgcatttgtcaaactaccaatagatt-cctgacgcagaattctttctctatcag

upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S199_57V6.1 (Physcomitrella patens), 5'ss of exon 6
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccatttt-------attacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct-------
 || |||||||| || ||||||||||| |||||||| || ||| | || |||||| | |||||||||||||||||||||||  | ||||| ||| | |||||   | | |  |   |  ||| |        |   |||       |   || |  ||  | || | |  |        |||| ||   | |  |  ||||| | ||       
TCCTGAATCTGATGTGTGGAGTATTGGTGTAATAACATACATTTTGCTCTGTGGACGGCGACCTTTCTGGGACAAAACTGAGAAGGGAATCTTTGATGAGgttcgtcttctgattgtcacttaggaaatttgctgctttcgaggagacagcagggtttggagtgttcatgaaatggccattgcattcttaacg-tgcattttttccttcatcag

upper sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ28817 (Selaginella moellendorffii), 5'ss of exon 5
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccattttattacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct
 ||||| || || ||||||||| | || || || || || ||  | || |||||||| ||||||||||||||||| || |||| |||||| || || |||||          || | | ||||   ||  | |     ||  | |   |||| |||  |   ||||                                  
GCCAGAGTCCGATGTTTGGAGTGTGGGTGTCATCACATACATATTGCTATGTGGAAGGCGACCTTTCTGGGACAAGACGGAAGCTGGAATCTTCAATGAGgt----------aagcaacctttcgattctagc-----tacgataaacgttttattcttctcaactccag------------------------------

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|33798127|gb|CF324924.1|CF324924
EST:     GTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAG                         GTGTTGAAAAACAAGCCAGATTTTCGTCGCAAGCCCTGGCCAAATATCACT
genomic: GTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgc ... tttggtgcagGTGTTGAAAAACAAGCCAGATTTTCGTCGCAAGCCCTGGCCAAATATCACT
EST: gi|58602510|gb|CK013038.1|CK013038
EST:     TTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAG                         GTGTTGAAAAACAAGCCAGATTTTCGTCGCAAGCCCTGGCCAAATATCACT
genomic: TTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgc ... tttggtgcagGTGTTGAAAAACAAGCCAGATTTTCGTCGCAAGCCCTGGCCAAATATCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAGAATCTGACGTTTGGAGTATTGGCGTAATAACCTATATTCTACTGTGTGGAAGACGACCTTTCTGGGACAAAACTGAAGATGGAATATTTAAAGAGgtcattttgcctaaactatctttgtcttacaaccattttattacatgtgtttcattgattaaaactattttcttgccttacaatcactatattttcttct

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA