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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatctcatcagattacggtaaaagcgcttcggtttttttgctgaaatccctttgctccgcgtgcag

Basic information

species Zea mays
transcript GRMZM2G044866_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044866_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 5'ss of exon 7
GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatctcatcagattacggtaaaagcgcttcggtttttttgctgaaatccctttgctccgcgtgcag--------
||||| ||||| ||||| || ||||| ||||||||||||||||| ||| |||| |||||||||||  ||||| |  ||||||||||||| || ||||| |||||||||||||||   | || ||  ||| |  ||| |||  |||     | |     ||  |    ||||         
GCTGGCAAGTATGACAATGCATCAATTGATTACCAAATAGAGTTTTACCGAAATGAGGGCCTAACATATTATACACCTGCTAAGCTTCCTATTACAAGTGgtcagtgatctcattgaagtatggcgaaaacagttcagttactttctgagattttaactgtcctttttgcattggtttag

upper sequence: GRMZM2G044866_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G53040.1 (Arabidopsis thaliana), 5'ss of exon 9
GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatctcatcagattacggtaaaagcgcttcgg----tttttttgctgaa--atccct-ttgctccgcgtgcag-----------
||  ||||||||||||| || ||||| ||||||||| ||||||||||||  || || ||  |||| | |||| |    ||||||||||| || ||||| ||| |  | | | | || || | | | | |  | | |      || || || | ||  ||| |  |||   |   |  |            
GCAAGAAAGTACGACAATGCCTCAATAGATTACCAAGTAGAGTTCTACAAGAAGGAAGGTTTAACACCTTATACGGAGGCTAAGCTTCCAATAACAAGTGgtaatggttttaaccatatgaggatgataaagttccacaattttcttctgttcaatgatcacaattgaaacatttcaaatcgtttggcag
















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|32936542|gb|CF041361.1|CF041361
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|71313493|gb|DR793305.1|DR793305
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|32936757|gb|CF041576.1|CF041576
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|83278829|gb|DV942837.1|DV942837
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|32936590|gb|CF041409.1|CF041409
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCCTCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|32936641|gb|CF041460.1|CF041460
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
EST: gi|32936797|gb|CF041616.1|CF041616
EST:     AAACGAGGGCCTAACGCATTATTCTTCTGCTGAGCTTCCCATCACAAGCG                         ATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC
genomic: AAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACC

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: 47 (upstream exon), 45 (downstream exon)
Score: 40

GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACCTGTTCACGTGCGTATGGTTCAATGAGGTTGATCGCTTCACCTCCAGGGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 22

GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACCTGTTCACGTGCGTATGGTTCAATGAGGTTGATCGCTTCACCTCCAGGGA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 25

GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACCTGTTCACGTGCGTATGGTTCAATGAGGTTGATCGCTTCACCTCCAGGGA


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 41

GCTGGAAAGTACGACAACGCGTCAATCGATTACCAAATAGAGTTCTACAGAAACGAGGGCCTAACGCATTATTCTTCTGCTAAGCTTCCCATCACAAGCGgtcagtgatc ... ccgcgtgcagATGTCCCCGAAGGCTGTGTGATCATCAGAGAGCACATCCCCATCACGAACCTGTTCACGTGCGTATGGTTCAATGAGGTTGATCGCTTCACCTCCAGGGA