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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccgacatcacttacatatattttcctctatggcaccctcagaagtactgaatatatttgcctctttccctgtttcag

Basic information

species Oryza sativa
transcript LOC_Os05g41110.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G123969_T01 (Zea mays), 5'ss of exon 3
ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccga--catcacttacatatattttcct---------ctatggcaccctcaga--agtactgaatatatttgcctctttccctgtttcag
|||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |||||||  ||   ||     || |  | | | | |  |          ||     |  || ||      |||| | |  | |    |  |   ||||||  
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctctccgcactctcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg-

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G044137_T01 (Zea mays), 5'ss of exon 4
ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccga-----catca-cttacatatatt-----ttcctctatggcaccctcaga--agtactgaatatatttgcctctttccctgtttcag
|||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |||||||  ||   ||     ||| | |||   | | |      |  | ||     |  || ||      |||| | |  | |    |  |   ||||||  
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctgtccgaactgtcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg-
















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|88208991|gb|CI208840.1|CI208840
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|30228744|gb|CB966634.1|CB966634
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88281712|gb|CI403108.1|CI403108
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|14981077|gb|BI305768.1|BI305768
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|25797182|gb|CA753143.1|CA753143
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|27578251|gb|CB000946.1|CB000946
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|30228625|gb|CB966515.1|CB966515
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|87025758|gb|CI282335.1|CI282335
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTG
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|87023003|gb|CI280020.1|CI280020
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|58594776|gb|CF993084.1|CF993084
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|87032220|gb|CI262002.1|CI262002
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86593179|gb|CI255641.1|CI255641
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|53553193|gb|CO435745.1|CO435745
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88995949|gb|CI037240.1|CI037240
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|29686201|gb|CB682476.1|CB682476
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86530215|gb|CI170421.1|CI170421
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|58031073|gb|CX728616.1|CX728616
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|87011660|gb|CI281362.1|CI281362
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86532355|gb|CI172561.1|CI172561
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88241578|gb|CI241427.1|CI241427
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86417527|gb|CI031736.1|CI031736
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88547996|gb|CI478330.1|CI478330
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88400326|gb|CI591016.1|CI591016
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGGCTCC-AGTGAAGA
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGA
EST: gi|86599456|gb|CI251414.1|CI251414
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88556598|gb|CI486936.1|CI486936
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86533322|gb|CI173528.1|CI173528
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|55410942|gb|CV723318.1|CV723318
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86416886|gb|CI030897.1|CI030897
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86835219|gb|CI346694.1|CI346694
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|86529357|gb|CI169563.1|CI169563
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
EST: gi|88991955|gb|CI035093.1|CI035093
EST:     TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTG                         GTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT
genomic: TGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 74 (downstream exon)
Score: 120

ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgct ... cctgtttcagGTGACTCGGACATCATCAACACAACCCCTGCCTCCCAGTGAAGAAGTTTTTACCTATTTAGTTGAGATGTAGGGTTCAGACGTGCTTACATGGCCAATGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccgacatcacttacatatattttcctctatggcaccctcagaagtactgaatatatttgcctctttccctgtttcag

- - - - - - - - - - - - - - - - - - - - - - TGCTGC