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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG

Basic information

species Zea mays
transcript GRMZM5G880102_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 12
gttatatggcattataaaagaaacattgatagctctatctgttgctgttca-gtgtagcgtagtgttcacgtgatcaat-tttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
||||||  |||  || |     | ||| | |  |  ||   ||| | || | ||| |  | | |  |    |  |     ||| ||||||||||| ||| |||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||||
gttataatgcacaatgaggaggatatttacatattcattcattgttattgaagtgcacagaaatcatggtattgttgtcatttgttcagGTCATTTCAGCAGGTGGACTTCATGTAGTAGGAACAGAACGTCATGAATCTCGCAGAATTGATAATCAG

upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 14
gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttatt-cagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
|| |  | |  |  | |     || |      |   ||   |||||||| |         | | || |  |||||| | | | | |||||  |   ||  || || || || |||||||| |||||||| |||||||||||  ||||||| ||||||
gtcaatttgtttcttgactagtacttcc----cctcatacattgctgttga------tacattattaa--tgatcattatgactgcagGTTGTGGAAGCTGGCGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG

upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 14
gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttatt-cagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
|| |  | |  |  | |   | || |      ||  ||   |||||||| |       | | | || |  |||||| | | | | |||||  |   ||  ||||| || || |||||||| |||||||| |||||||||||  ||||||| ||||||
gtcaatttgtttcttgactaatacttcc----cttcatacattgctgttga------tgcattattaa--tgatcattatgactgcagGTTGTGGAAGCTGGTGGACTACATGTAGTAGGCACAGAGCGTCATGAATCACGTCGAATTGATAATCAG

upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 13
gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
||||  |    ||| |  |||    |   |   |||  ||||      ||  ||| |   |  ||| |        |  |  | |||||  |   ||  ||||| |||||||| || || |||||||| |||||||||||  |||| |||||||||
gtta-gttctgttacagcagagcagtatgtgaatct--ctgtcaagtgtc--tgttgttgatcgtttattctcctgaactgctgcagGTGGTGGAAGCTGGTGGACTTCACGTGGTGGGGACAGAGCGGCATGAATCACGTCGAATAGACAATCAG

upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08380 (Selaginella moellendorffii), 3'ss of exon 13
gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
                                        |||      ||  ||      |  ||  | | ||   |||  | |||||  || | | |||||| ||||||||  |||| ||||||||||| |||||||| |||||||| ||||||
----------------------------------------gttagaagccaaagttttcatgatttgtcctcatagttttcttgcagGTTGTTGCTGCAGGTGGCCTTCACGTGATAGGCACAGAGCGCCACGAATCACGAAGAATTGATAATCAG

upper sequence: GRMZM5G880102_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ15249 (Selaginella moellendorffii), 3'ss of exon 13
gttatatggcattataaaagaaacattgatagctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
                                        |||       |  ||      |  ||  | | ||   |||  | |||||  || | | |||||| ||||||||  |||| |||||||||||||||||||| |||||||| ||||||
----------------------------------------gttagaaacgaaagttttcatgatttgtcctcatagttttcttgcagGTTGTTGCTGCAGGTGGCCTTCACGTGATAGGCACAGAGCGCCATGAATCACGAAGAATTGATAATCAG

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|226431424|gb|GO477760.1|GO477760
EST:     TGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAG                         GTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCA
genomic: TGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAGgttatatggc ... ttttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCA




















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: 48 (upstream exon), 46 (downstream exon)
Score: 51

GGACCAACACGTGATGAAGTAATAGCGAATTTGAGAAATGCATTTGTGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAGgttatatggc ... ttttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

GGACCAACACGTGATGAAGTAATAGCGAATTTGAGAAATGCATTTGTGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAGgttatatggc ... ttttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

GGACCAACACGTGATGAAGTAATAGCGAATTTGAGAAATGCATTTGTGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAGgttatatggc ... ttttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 87

GGACCAACACGTGATGAAGTAATAGCGAATTTGAGAAATGCATTTGTGAAGATAGCAGACGAATATAAAGTTTACACTGAGGAGGAAAAGCAGAAGgttatatggc ... ttttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatctgttgctgttcagtgtagcgtagtgttcacgtgatcaattttattcagGTCATTACAGTAGGTGGGCTTCACGTAGTAGGAACAGAGCGCCATGAATCACGCAGAATTGACAATCAG
                                             ttttattc  CT-rich tract
                                      tgatcaattttatt  TA-rich tract