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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgatatttatgcatttaaacatccatatgatcgtccttgcag

Basic information

species Zea mays
transcript GRMZM2G359234_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 5'ss of exon 4
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacata--------ttatagactatt--tttcttagttgtgatatttatgca----tttaaacatccatatgatcgtccttgcag
||||| ||||| || ||||||||||||||||| ||||| ||||| || || ||||| |||||||| |||||||||||||| |||||| ||||   || ||        ||||  ||| ||  || |  | ||| | | |  ||       | | |   |  | |||||  || ||| ||
GTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAGgttcgtttaacacgtaccgctattttattaacttttggttacacatttgcgctgtcaatatgaaattctgagtttatacatgattatcattgtag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G05260.1 (Glycine max), 5'ss of exon 4
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgat-----atttatgcatttaaac-atccatatgatcgtccttgcag
|| |||||||| || |||||||| |||||||| || || |||||  | || ||||| ||||| || |||||||||||||||||||||||  |      |  | ||    |||| || |  |||||       |||| ||   ||| || ||  || |     |  || |||
GTTCGTATTGCTCGAATTTTCAACACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTTGTTAGCAATTTTGTTGCACAGgtttgactttcttgtcct-tatttaatttgtcattattgtggagagcaatttgtgttcttatactatttatttacatatgtttccag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G19640.1 (Glycine max), 5'ss of exon 4
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgat-----atttatgcatttaaac-atccatatgatcgtccttgcag
|| |||||||| || ||||||||||||||||| || || |||||  | || ||||| ||||| || ||||||||||||||||||||||| ||      |  | ||   | ||| || |  |||||       | || ||   ||| || ||  || |  |  |  ||||||
GTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAGgtttgattttcttgtcct-tattttttttgtcattattgtggagaggaacttgtgttcttatactatatatttatttatgtttgcag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatat---tatagactatttttcttagttgtgatattt---atgcatttaaacatccatatgatcg------tccttgcag
||  | ||||| ||||||||||| |||||||| ||  | |||||||| || ||||| ||||| || || || |||||||| |||||||   | || |||     || |||| |    | |    |      |||   |  || |   |||    |||  | |      ||  |||||
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 5'ss of exon 5
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgct--acatattatagac-tatttttcttagttgtgatatttatgcatttaaacatccatatgatc------gtccttgcag----------------------
|| ||||| || || ||||||||||||||||| |||||||||||  | || ||||| |||||||| ||||||||||||||||||||||| |  |   || |||| |      | || |   |      ||          ||| ||||   ||| |        ||  ||  |                       
GTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAGgtttgatctcctgacttattttccttacagttctgccaaacacaatgaaccgaatcttagacatttttataagttctaaagtttttttaactgttatagctatgttttgcag

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgatatttatgcatttaaacatccatatgatcgtccttgcag
||| | || || ||||||||||| |||||||||||| | |||||||| |||||||| || || |||||||| || || || |||||          |||    |  |    || |    ||| | ||  || ||| ||    ||                     
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtaca---aaagcatcccttgaaaagcttcttcccgttttcattcttttgctttctcgcag--------------------

upper sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ30517 (Selaginella moellendorffii), 5'ss of exon 5
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgatatttatgcatttaaacatccatatgatcgtccttgcag
||| | || || ||||||||||| |||||||||||| | |||||||| |||||||| || || |||||||| || || || |||||      || |    ||  | |    || |    ||| | ||  || | | ||    ||                     
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc-atccgttgaaaa--gcttcttcccgttttcattcttttactttctcgcag--------------------

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|60345409|gb|DN212382.1|DN212382
EST:     CTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAG                         GCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA
genomic: CTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA
EST: gi|78123100|gb|DV541484.1|DV541484
EST:     CGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAG                         GCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA
genomic: CGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA
EST: gi|71305243|gb|DR788759.1|DR788759
EST:     CTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAG                         GCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA
genomic: CTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGA

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: 46 (upstream exon), 47 (downstream exon)
Score: 47

GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGAAGTTTCCAATATGTTGCTGATCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 223

GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGAAGTTTCCAATATGTTGCTGATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGAAGTTTCCAATATGTTGCTGATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgc ... gtccttgcagGCACTGCGAAGGCAACCGATGACAGTCTATGGTGACGGAAAACAAACTCGAAGTTTCCAATATGTTGCTGATCTG