Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57790.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||| |||||||||| |||||||||||||||||||||||||||||||| |  ||| |                  |||  |  | ||||||    |||| | || |||| |    || || |       || |  | ||||         |||||||           | ||| |  | |         ||| ||  |  ||| || | ||||| |||||
TGATGCGGGACTTCAAGCGCCTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGTACGACAACAATATCATGCTCTGGAACGCCGTCATATTCGGgtatcagcccgcctatt-------------tctgtgatgttaggttagctagcctaagg-atctagtgaggcgtgaggccgcgatacttttggtggg--------ttttaat-----------gctgactgtgct---------ttttctcttggtgtttgttgcgattctgcag

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
|||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||             ||| ||    |||  |  | ||||||    |||| | || ||||      |   | |  |    || |    |||  |    |  ||||  | |    ||| | ||| |  | |||||  |                                  
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatca------------ggccgcctatttctgtgatgttaggttagctagcctaagg-atctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctat----tgtcgtttgttgcgattctgcag----------------------------------

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgagg----ggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
||||||| ||||||||||| |||||||| || || || ||||| ||||||||||| ||||| ||||||||||||||| | ||||| || |||||||||||||    |||||  | ||    | |   || |       |||   || ||  |    |     | |  |||  | ||  |    ||| |    || ||| |  ||                                                                           
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgt----acccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt---------------------------------------------------------------------------

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
||||||| |||||||||||  |||| || || || || ||||| ||||||||||| ||||| |||||||| |||||||| ||||| || || ||||||||||| | |    | | || | |   |  |  |         |  ||   |  |  | | |||  |||| | || || ||    |     ||| |  | ||   ||||                                                                     
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgc-ctccctggtttcgttttttgttca-attgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgca----cgtcggagtgtcggtttt---------------------------------------------------------------------

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
||||||| ||||||||||| || || || || || ||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||  |   |  |||  | | |||     | ||     |||  | ||||   ||      | | ||||                                                                                                          
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgc--tcggcactagggtatcgat--ctaactcttggtttcg------tgttgcag----------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag
||||||| ||||||||||| || || || || || ||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||  |   |  |||  | | |||     | ||     |||  | ||||   ||      | | ||||                                                                                                          
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgc--tcgacactagggtatcgat--ctaactcttggtttcg------tgttgcag----------------------------------------------------------------------------------------------------------

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|218479910|gb|FG956825.1|FG956825
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGAC-CGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38479547|gb|CF963650.1|CF963650
EST:     GCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCGATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTC-ATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|11025772|gb|AU162373.1|AU162373
EST:     ACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: ACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|27576870|gb|CA999564.1|CA999564
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58688873|gb|CK077560.1|CK077560
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|27576883|gb|CA999577.1|CA999577
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|27576871|gb|CA999565.1|CA999565
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|3761950|gb|C99198.1|C99198
EST:     GGCGCGCCGCACGACAACAACTTCATGCTCTGGAACGCCGTCATATTCGGG                         ACCGGATGACACGCCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTC-GGgtagccaccc ... gattttgcagACCGGATGACACG-CCGTGGGATGGAG
EST: gi|426691|gb|D22760.1|D22760
EST:     GGCGCGCCGAATGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|8251184|gb|AU091335.1|AU091335
EST:     GGCGCGCCGCACGACACCAACATCATGCTNTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|33795388|gb|CF323564.1|CF323564
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58590675|gb|CF988983.1|CF988983
EST:     GGGGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38470097|gb|CF954228.1|CF954228
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|55411803|gb|CV724179.1|CV724179
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58677295|gb|CK065982.1|CK065982
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38475004|gb|CF959137.1|CF959137
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|55409133|gb|CV721509.1|CV721509
EST:     GGAGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAT
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|86419732|gb|CI054533.1|CI054533
EST:     GCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|425985|gb|D22670.1|D22670
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218485740|gb|FG958740.1|FG958740
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38482332|gb|CF966375.1|CF966375
EST:     GGCGGGCGGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38480664|gb|CF964753.1|CF964753
EST:     GCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|8336757|gb|BE041059.1|BE041059
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38469192|gb|CF953323.1|CF953323
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38468296|gb|CF952427.1|CF952427
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38469613|gb|CF953744.1|CF953744
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38468844|gb|CF952975.1|CF952975
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|38481856|gb|CF965925.1|CF965925
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|218505167|gb|FG956727.1|FG956727
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|42592241|gb|CK738727.1|CK738727
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|29666285|gb|CB662560.1|CB662560
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG
EST: gi|58585769|gb|CF984077.1|CF984077
EST:     CGCCGTCATATTCGG                         ACCGGATGACACGCCGTGGGATGGAG
genomic: CGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG

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: 75 (upstream exon), 75 (downstream exon)
Score: 336

TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccaccc ... gattttgcagACCGGATGACACGCCGTGGGATGGAG




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