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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagcccccccggcccccgtcgctcattcaattcatggcggcgtctcgaccagtgttactgactgtccctccgcgtgtcggcgcgccggacag

Basic information

species Zea mays
transcript GRMZM2G067022_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 4
CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc-----ccggcccccgtcgctcatt-caattcatggcggcgtc--tcgaccagtg-ttactgactgtccctccgcgtgtcggcgcgccggacag----------------------------------------------------------------------------------
|||||| | ||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||||||||| || |      || || ||||||        || |||      | ||   || |   || ||    ||  |   |    |  | |  ||   |   |                                                                                   
CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag

upper sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 5'ss of exon 3
CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagcccccccggcccccgtcgctcattcaattcatggcggcgtctcgaccagtgttactgactgtccctccgcgtgtcggcgcgccggacag
 || || | |||||| |||||  | ||||| ||||||||||| |||||||||||||||||||| |||||||||||||||||| |     |||| || |||||  | || |        |     | ||| || | | |          |   | |   || |  |||  ||    |  | |  |          
ACCATCTTTCCACAATTACCGTATTTGGTCTTTCCTCGGCCTTGGCATGACCACCTACACCGCTTGGTACCTCACCATCGCCTCTTTTCTCCATGGTCAGgtatgtcctcatcaaaatca--aatgatttaaatgaagaaaaaacaatg-tgacttaaaccggttgtaacttactggtttgtag----------

upper sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 4
CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagcccccccggcccccgtcgctcattcaattcatggcggcgtctcgac---cagtgttactgactgtccctccgcg--tgtcggcgcgccggacag-
||| || |  |||||||| || || ||||||||||||||| | || |||||||| ||||| ||||||||| | |||||||| |||  |||||||||||||||            |         ||   ||| |     |   |||| | |   |  | |  |   || | | | | |   | ||  | | |   || | 
CCCGTCTTTTCACAACTATCGAGTGTGGTCCTTCCTCGGCTTGGGGATGACCACTTACACGGCCTGGTACATGACCATCGCTGCGATCGTCCACGGCCAGgtagagaagaagaacaaagaaaaatctcccaaattcccactttgtcttgtcttcctctctctcgcgctattcgttctctcctttctccccacaacacgga

upper sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 4
CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagcccccccggcccccgtcgctcattcaattcatggcggcgtctcgac-----cagtgttactgactgtccctccgcgtgtcggcgcgccggacag-
||| || |  |||||||| || || ||||||||||||||| | || |||||||| ||||| ||||||||| | |||||||| |||  |||||||||||||||            |         ||   ||| |     |   |||| | |     |  | |  |   || | | | | |   |     | |   |||  
CCCGTCTTTTCACAACTATCGAGTGTGGTCCTTCCTCGGCTTGGGGATGACCACTTACACGGCCTGGTACATGACCATCGCTGCGATCGTCCACGGCCAGgtagagaagaagaacaaagaaaaatctcccaaattcccactttgtcttgtcttcctctctctctcgcgctattcgttctctcctttctccccacaacacg

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|87156542|gb|DY401331.1|DY401331
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCGGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
EST: gi|26559840|gb|CA832075.1|CA832075
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCGGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
EST: gi|78087017|gb|DV515410.1|DV515410
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCTGGCCCCAGTCA-GCTCGTGCCCTACTTCAC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAG-CAAGCTCGTGCCCTACTTCAC
EST: gi|91870569|gb|EB400953.1|EB400953
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
EST: gi|91871140|gb|EB401266.1|EB401266
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
EST: gi|22819244|gb|BU499334.1|BU499334
EST:     CGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCGGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
EST: gi|211191277|gb|FL124541.1|FL124541
EST:     CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAG                         GTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC
genomic: CCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACC

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: 43 (upstream exon), 45 (downstream exon)
Score: 11

CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGT


Block sizes: 24 (upstream exon), 26 (downstream exon)
Score: 1

CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 13

CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 8

CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc ... cgccggacagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGT