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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaatcattttggtgttatttgttgttctatcaattatatcgtgctcacactttaaattgtatcaaccgttttcag

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 7
GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactga--atcattttggtgttatttgttgttct--atcaattatatcgtgctc--acactttaa-attgtatcaaccgttttcag
| |||| |||||| ||||||||||| ||||||||||||||| |||||||| ||||||||||||||||||| |  |   || ||| |||  ||||   | |  | || || | |   |||   |  |||||| | ||      || |||||||
GATTGGCTTGCTGTCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAGgtatactcatgacacttctggcgttgcttgtacatattgaccagttctttaaggctgtaatcctttaataatgctatgtccattttcag

upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G61250.1 (Arabidopsis thaliana), 5'ss of exon 6
GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatact----gaatcatttt--ggtgttatttgttgttctatcaa-----ttatat-cgtgctcaca--ctttaaa--ttgtatcaaccgttttcag
||||||||   || || ||||||||| |||| || |||||||||||||||||||| || |||||| |  |     | ||  |||    ||||  ||||| |||| | |      ||| || | |  | |||  ||| | |  |||  |  |   | |||||
GGTTGGTTCTTTGTCTTTTCTGGAATATCATCGCCGTTACTACAGCTTGGATCAAAGGAGAAGgtttgtttcttaagtctatttcaaatgttgcttgttcttctgtaagagaccttaaatgcatattaacaggcttaagagtttggttttattttgttcag

upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 6
GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatact--gaatcattttggtgttatttgttgttctatcaattatatcgtgctcacactttaaattgtatcaaccgttttcag--
| |||||    |||||    |||||| |  |||||||||| ||||||||||| ||||||||||||    |  |||   | ||    |         |       ||| || | | |    | |     ||| ||   |  |  |     
GTTTGGTACTTTGCCTTACATGGAATATTGTAGCAGTTACCACAGCTTGGATTAAGGGGGAAGgttagtttggaactttgttcacctcccaaaccttggggaatattgtaaccttccataattgggtcttgaatttgctttccttgtag

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|76929603|gb|DV172080.1|DV172080
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     CCTCTTCTGGAATCTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGGTTGTTGGCAATAATCTACTTC
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGG-TTGTTGGCAATAATCTACTTC
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG                         GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG
genomic: CCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 65

GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 126

GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG


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

GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 178

GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAGgtatactgaa ... ccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG