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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca...

Basic information

species Oryza sativa
transcript LOC_Os01g60190.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G003385_T02 (Zea mays), 5'ss of exon 6
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgactggtgacttagtaa--tttttgaggtacttaggccataagggagttgattca-
||||||||||||| || |  |||||||| ||||||||||||||||| ||||||||||| || |||||||| ||||||||| |||||||||| ||||||||||||||||      ||   |   | |||   ||||||      |  | |||    |  | ||||   | |||||  |  || | ||  |  |  || |||   
AGTTGAAGCTTCCAAGTCGCTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtactatatgtctttcagcccttctcttgataccttttttgctcactt-caatatcgtaaatctcttgagtcatctaagtcagcatcg--ttcatttgt

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G833389_T02 (Zea mays), 5'ss of exon 6
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgact--ggtgacttagtaatttttgaggtacttaggccataagggagttgattca
||||||||||||| |||| ||||||||| ||||||||||||||||| ||||||||||| || |||||||| ||||||||| |||||||||| ||||||||||||||||      |  | |   |||||   |||||||     |||| |||    |  | ||  |    ||    |   |  | |||    |     || | 
AGTTGAAGCTTCCAAGCCGTTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtactatctatttctcagcctttctcttgatacttttt-tatttacttcaatatcgtaaaatcacttagtttttctgagtcatctaagtcagcatgc-

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G40690.1 (Glycine max), 5'ss of exon 5
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctcttt-cctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca--
| ||||| ||||| || ||||||||||| || ||||||||||| || || || ||||||||||| || ||  | |||||  | || || || ||||||||| |  |  ||   ||  |||| | ||   |  |  ||  |    ||||     || | |||   |         |||||   || |        || ||    
AATTGAAACTTCCAAGTCATTACCTTGTTTCTCCACCAGAGATTGACAGGACTTCTGGTGAATATTTAGTGTATAATGGTATTCGGACTTTTGCTTGCAGgtagttgtct--tttatcactattttaatcgttagtaggatttttattatactgtaatttatggaagaccataatacttctacc-tgcttattctgtttttgt

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 5'ss of exon 5
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaag-tacctggcttcccactctctt-tcctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca
||||||||||||| |  ||||||||||| || || ||||||||||||||||||||||||||||| || ||  | ||||| || || || || ||||||||| ||| |  | |       | | | || || ||    ||||||| || | | |  |   |    || ||      |  ||       |      || |||  
AGTTGAAGCTTCCCAATCATTACCTTGTTTCTCCTCCAGAGATAGAGAGAACATCTGGTGAATATTTAGTGCACAATGGTGTTCGTACTTTTGCTTGCAGgtaaggtggcagataatgaattgtgttatcatcaagaactaaaattaattattattatttgttgaagttaactatttgttctttttcatcaacattcatt--

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ14459 (Selaginella moellendorffii), 5'ss of exon 5
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca
||||||| ||||| |   | ||  | ||    || || || || |||||||| |||||||| |  ||||||||||| |||||||| || |||||||||||| |||    |  ||   |  |    |   || | |||||||  | |    | |                                               
AGTTGAAACTTCCCACGAAGTATTTAGTTGATCCCCCGGAAATTGAGAGAACCTCTGGTGAGTTTTTGGTAAAGAACGGCGTCCGGACTTTCGCTTGCAGgtaaga--tttactcttctttgcaatgtatccgctactaaac-tgtctctttgcag--------------------------------------------

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ26058 (Selaginella moellendorffii), 5'ss of exon 5
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca
||||||| ||||| |   | ||  | ||    || || || || || ||||| |||||||| |  ||||||||||| |||||||| || |||||||||||| |||    |  ||   |  |    |   || | |||||||  | |    | |                                               
AGTTGAAACTTCCCACGAAGTATTTAGTTGATCCCCCGGAAATTGACAGAACCTCTGGTGAGTTTTTGGTAAAGAACGGCGTCCGGACTTTCGCTTGCAGgtaaga--tttactcttctttgcaatgtatccgctactaaac-tgtctctttgcag--------------------------------------------

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|58596168|gb|CK006696.1|CK006696
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|9788888|gb|BE530898.1|BE530898
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|163921118|gb|EG710144.1|EG710144
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|38476992|gb|CF961125.1|CF961125
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATT
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATT
EST: gi|38479186|gb|CF963319.1|CF963319
EST:     CATCTGGTGAATACTTGGTAAAGAATGGCGT-CGCACCTTGGGGTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGAT
genomic: CATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTT-CGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGAT
EST: gi|33678746|gb|CF306985.1|CF306985
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|33679927|gb|CF308166.1|CF308166
EST:     AAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: AAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|157650077|gb|EX449711.1|EX449711
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|29687456|gb|CB683731.1|CB683731
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|29616025|gb|CB621037.1|CB621037
EST:     ACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|58695777|gb|CK084464.1|CK084464
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|29687056|gb|CB683331.1|CB683331
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|27577152|gb|CA999846.1|CA999846
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATC
EST: gi|29679426|gb|CB675701.1|CB675701
EST:     ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAG                         TGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAAACG-AAACCGAT
genomic: ACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacct ... ttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAA-CGGAAACCGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGAAGCTTCCGAGCCATTACCTTGTCTCCCCACCAGAGATAGAGAGAACATCTGGTGAATACTTGGTAAAGAATGGCGTCCGCACCTTCGCTTGCAGgcaagtacctggcttcccactctctttcctctgatactaaaaatattgactggtgacttagtaatttttgaggtacttaggccataagggagttgattca

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