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'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctattattttcaattttcatctgtttaagattaagatgcatgatgtgattatactgagctgcatgatgtgattaatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 7
gtattctattattttcaattttcatctgtttaagattaagatgcatgatgtgattatactgagctgcatgatgtgattaatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA
|||   |||| |||||| ||||| |       |||| | | |||||  | || ||| |||||| |   |        ||||||  ||||||||||||| || |||||||| |||||||||||||||||||||||||||||||| ||||
gtagg-tattcttttcagttttcgttc-----agatca-gttgcatactttggttaaactgagttttgta-------taatattgcagCCAGAGATATCCAAGCTTGGGAAACTATACCTCTTGGACCTTTCCTTGGGAAAAGTTTCA
















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|32937713|gb|CF042532.1|CF042532
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|149089319|gb|EE178541.2|EE178541
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGNACCTT
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTT
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     TAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTNGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         -CAGANATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     GATGAATGA-TGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: GATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|149094603|gb|EE180134.2|EE180134
EST:     TGATGCTGAAGAACATATTTTTGGGCTACCTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTC
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTC
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     TGATGCTGAAGAACATATTTTNGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
EST: gi|149106513|gb|EE188405.2|EE188405
EST:     TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCCTTGG-
genomic: TGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCC-TTGGG
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     GATGCTGAAGAACATA-TTTTGGCCCTAACTTTGATGAATGATTGGAGCG                         CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA
genomic: GATGCTGAAGAACATATTTTTGG-CCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGA

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), 49 (downstream exon)
Score: 119

GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 99

GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 160

GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAATGATGCTGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGCGgtattctatt ... aatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaagatgcatgatgtgattatactgagctgcatgatgtgattaatatgtcagCCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA
                                         gattaat  putative branch site (score: 160)
                                        tgattaatat  TA-rich tract