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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatgtggcaccactgcattgcatttttaattgtttcttctatcaattgcagtctgtttttttttgctttgcttactcattgctttaattactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 4
tatatgtggcaccactgcattgcatttttaattgtttcttctat-caattgcagt-ctgtttttttttgctttgcttactcattgctttaattactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA---
     |     ||  | | || | |||||  |       | |   ||||   |||  |   | ||||  | ||| ||||  ||||||||| || || ||||||| ||||||||||||||||||| | || |||| |||||||||||   ||| |  |||| ||| | | ||||| || ||| ||||||||| ||||||||||   
--cgagctatgccttttcttttcttttttcctcacaaaatatccacaatccaagtattagctgttttgaccttggttacatattgctttacttcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGA---TTCACGGAGTGTAGGGACTGGTACCTCTTCTAGTGCAAGTACTAGTAGTTCTAGGG
















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|31352864|gb|CD437221.1|CD437221
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|149084056|gb|EE173454.2|EE173454
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGAAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA
EST: gi|19822590|gb|BQ048614.1|BQ048614
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|71419454|gb|DR804774.1|DR804774
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211384020|gb|FL015615.1|FL015615
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAAATTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211386656|gb|FL015629.1|FL015629
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|78112474|gb|DV530868.1|DV530868
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211384019|gb|FL015614.1|FL015614
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|9732635|gb|BE511387.1|BE511387
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|50332602|gb|CO527728.1|CO527728
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|19822589|gb|BQ048613.1|BQ048613
EST:     ATGCTCTCTCCCTTTTGNCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
EST: gi|211386648|gb|FL015621.1|FL015621
EST:     GCTCTCTCCCTTTTGTCTACAANTGATAAAACA-TAAAAATACTGGAAAG                         GGTCA-GAGA-GAAAGTAAAACGATTTGCAGTCATGAAATTTGGACA
genomic: GCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAA-TACTGGAA-Ggtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA-TTTGGACA
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAAATTTGGACAGNTC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAA-TTTGGACAGTTC
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC
genomic: ATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCC

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), 45 (downstream exon)
Score: 101

GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 127

GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 131

GGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggatgc ... tactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcagtctgtttttttttgctttgcttactcattgctttaattactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA
            tttttttttgcttt  TA-rich tract