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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag

Basic information

species Zea mays
transcript GRMZM2G007260_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag
||||||| |||||||||||  ||||||| || || || ||||||||||||||||| ||||| ||||||||||||||| | ||||| || ||||||||||||||  ||  |  |     ||   ||| || | |  ||  ||  ||     ||    |||  ||    | ||| | |  || || ||   |     ||    ||||| ||               
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcc-----tccccgattttcgttctgcatgctcaa----ttgtgtcggtatgaatgcgaaattcgtggggcgcggag-atttgcatggcggtgtcggttt--------------

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag
||||||| ||||||||||| ||||| || || || || ||||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||||||||||||  | |   |    |  | |  | ||  |||   | |  |  ||   || || ||           ||| |    || |  |   | ||   |   | ||||| || |             
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcgg-----------aattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt-------------

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgta---atcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag
||||||| |||||||||||  | || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||   ||   |||||      ||  | | |     || ||  | |       || ||  |                                                                  
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaact--cttggtttcgtgttgcag------------------------------------------------------------------

upper sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgta---atcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag
||||||| |||||||||||  | || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||   ||   |||||      ||  | | |     || ||  | |       || ||  |                                                                  
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaact--cttggtttcgtgttgcag------------------------------------------------------------------

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|211209634|gb|FL170002.1|FL170002
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|22521069|gb|BU079880.1|BU079880
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211209639|gb|FL170007.1|FL170007
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211212202|gb|FL170018.1|FL170018
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211209635|gb|FL170003.1|FL170003
EST:     GGCGCGCCS-ACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTTGGAC
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGAC
EST: gi|211209646|gb|FL170014.1|FL170014
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211416709|gb|FL320472.1|FL320472
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211209638|gb|FL170006.1|FL170006
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211209637|gb|FL170005.1|FL170005
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|149074449|gb|EE162844.2|EE162844
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211209642|gb|FL170010.1|FL170010
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|211212201|gb|FL170017.1|FL170017
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|14701443|gb|BI233861.1|BI233861
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG
EST: gi|20803162|gb|BQ294212.1|BQ294212
EST:     GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGG                         GCCGGATGACACGCCGTGGGACGGAG
genomic: GGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG

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: 49 (upstream exon), 40 (downstream exon)
Score: 19

TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 40

TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtaatcaggc ... gattctgcagGCCGGATGACACGCCGTGGGACGGAG




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