Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtccctttttctccctaaaatttgagctactagatattttagttacaagttcagctgatgtatgttatgtgcccatgttttag

Basic information

species Zea mays
transcript AC209858.4_FGT002
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209858.4_FGT002 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g05720.1 (Oryza sativa), 5'ss of exon 11
GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtccctttttctccctaaaatt--tgagctactagatattttagttacaagttcagctgatgtatgttatgtgcc-catgttttag
|||||||||||| ||||||| |||||||| || ||||||||||||||||||||| |    | | |||||   | |||| |  |   | |  | | | | | | ||| |||||      |  |||| |  | || | | |  |||
GAATGCAAGGATGCTATAGGTTTCAACCTTGCTGCAATGGATCATATAAAAgtaagattccgccttttccatcaaaaactccttttccatcaaaaactcttgctactagttcttaactttgatgtgaaatccctcttctgctag
















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|32937153|gb|CF041972.1|CF041972
EST:     AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
EST: gi|32932056|gb|CF036868.1|CF036868
EST:     AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
EST: gi|37399955|gb|CF637321.1|CF637321
EST:     AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCATTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
EST: gi|166437833|gb|EG112297.1|EG112297
EST:     TGCAAGGATAACTATAGGCTTCAACCTCGCCGCAATAGGATCATATAAAA                         GAATTGTTGGC
genomic: TGCAAGGATA-CTATAGGCTTCAACCTCGCCGCAAT-GGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGC
EST: gi|211417128|gb|FL448753.1|FL448753
EST:     AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
EST: gi|78084366|gb|DV512759.1|DV512759
EST:     AAAGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
EST: gi|211057077|gb|FL049064.1|FL049064
EST:     AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAANA                         GAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCG
genomic: AATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCG
EST: gi|78084367|gb|DV512760.1|DV512760
EST:     ATGCAAGGATACTATAGGCTTTCA-CCTCGCCGCAATGGATCATATAAAA                         GAATTGGTTGGCCGTTGAGATCAGATG
genomic: ATGCAAGGATACTATAGGCTT-CAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTG-TTGGC-GTTGAGATCAGATG
EST: gi|166634734|gb|EG179420.1|EG179420
EST:     CTCGCCGCAATGGATCATATAAAA                         GAATTGTTGGCATTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA
genomic: CTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAA

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: 49 (upstream exon), 46 (downstream exon)
Score: 57

GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAACTCATGGAAATCAAGAAGGAGCAGTCGAAGCGGTCAAGTAGTAGGCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 24

GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAACTCATGGAAATCAAGAAGGAGCAGTCGAAGCGGTCAAGTAGTAGGCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAACTCATGGAAATCAAGAAGGAGCAGTCGAAGCGGTCAAGTAGTAGGCTTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 24

GAATGCAAGGATACTATAGGCTTCAACCTCGCCGCAATGGATCATATAAAAgtacggggtc ... catgttttagGAATTGTTGGCGTTGAGATCAGATGCACCTTTCCGTGATGCCAAGGCGAAACTCATGGAAATCAAGAAGGAGCAGTCGAAGCGGTCAAGTAGTAGGCTTG