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

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcag

Basic information

species Zea mays
transcript GRMZM5G841900_T05
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 5'ss of exon 1
CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggtt--------------ggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcag
|   || || |  ||||||||||||||||| ||||  |||||||||||  |||| || |  |||||| ||||||||||  | || ||||||  ||| |||||||||||              |  ||||| | |  || |||| |  ||    | ||  | ||| |  ||||||| |    ||| ||||||||
CCTAGCGGGGCTCGGCGCCTACGCCGACGGCCGCTGCGTGCGCGCGTCCATCACTGGCCATCGCCGCCTCGTGCCGCCTCCTCCCGGCTCCACCGATCAGgtagggttcagctagggttttggatttggtggcgcctcggattcctcttctgatggtctgcgtggttggttggttcg---attttggctgcag
















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|211102908|gb|FK962289.1|FK962289
EST:     TCACCGGGCGCCGCCGCATCGTGCCGSCCKCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102904|gb|FK962285.1|FK962285
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCNCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118858|gb|FL110173.1|FL110173
EST:     TCACCGGGCGCCG-CGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118856|gb|FL110171.1|FL110171
EST:     TCACCGGGCGCCGCCGCAYCGTGCCGCCCGCACCTGCCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102909|gb|FK962290.1|FK962290
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGASGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102911|gb|FK962292.1|FK962292
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGSACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|148939988|gb|EC884719.2|EC884719
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGGCTGCAG                   
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A--C--CAGgtagggttgg ... tggg
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     CACCGGGCGCCGSCGCATCGTGCCGCCMGCACCTGGCTCCGACGAACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACA
genomic: CACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGA-CCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCA
EST: gi|211118857|gb|FL110172.1|FL110172
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG

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 2 RNA-Seq libraries.


Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 2

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 4

CGCGGCCGGACGTGGCGCCTACGCCGACGGTCGCTCTGTGCGCGCGTCGGTCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA




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