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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag

Basic information

species Zea mays
transcript GRMZM2G074479_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgt-taatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag
||||||||||||||| ||| |||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |       ||       |    | |||   |  |  |||| | |   | ||| |||      | |      |||     |||||||||||||   ||                                                                                                     
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgtcagccatggacgcggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg-----------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtcccctcccc--tcccccctcc-----cccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag
||||||| ||||||| |||||||||||| || || || ||||| ||||||||||| ||||| ||||||||||||||| | ||||| || |||||||||||||| ||   | |||||||  |   |  ||      | | |||  ||        |  ||     | ||| |  ||   ||     |   | | | || ||                                                                                                           
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt-----------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag
||||||| ||||||| |||| |||| || || || || ||||| ||||||||||| ||||| |||||||| |||||||| ||||| || || ||||||||||| |      ||||||      | |     | ||   ||    | |   ||     |  ||| | ||     |  |        |    ||  || ||  ||  |                                                                                              
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggtttcgttttttg-ttcaattgtgtc-cggtcgtggtgc--ggaattcgccgggcgtggg---aggcgcacgtcggagtgtcggtttt---------------------------------------------------------------------------------------------

upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcc-cgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||    ||  || | |  | |        |||| |   |           |   |                                                                                                                                                
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag----------------------------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcc-cgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||    ||  || | |  | |        |||| |   |           |   |                                                                                                                                                
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag----------------------------------------------------------------------------------------------------------------------------------------------

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|18964126|gb|BM660824.1|BM660824
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|19351561|gb|BM896093.1|BM896093
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|211348190|gb|FL266275.1|FL266275
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|18964589|gb|BM661093.1|BM661093
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: G-CGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|9824941|gb|BE575038.1|BE575038
EST:     CGCGCCGCACGACAACAACATCATGCTCTGNNGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: CGCGCCGCACGACAACAACATCATGCTCTG--GAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|18964591|gb|BM661094.1|BM661094
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|211348193|gb|FL266278.1|FL266278
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|18964127|gb|BM660825.1|BM660825
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|211353005|gb|FL266309.1|FL266309
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG
EST: gi|211280163|gb|FL132357.1|FL132357
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGATACGCCGTGGGACGGTG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 990

TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1925

TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2542

TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1614

TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcccgtc ... ggtttcgcagGCCGGATGATACGCCGTGGGACGGTG