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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaagataacacgtgttgaagcataccctttgcaaggtctcactgatatcacctttaattgctag

Basic information

species Zea mays
transcript GRMZM2G102858_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 11
TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaagataacacgtgt---tgaagcataccc-tttg--caaggtctcactgatat---cacctttaattgctag
||||||   ||||||||||||| ||||| || |||||||||||| | || ||||| || |||||| |||||||||| || |||  ||| |||||||||||||||        |||   ||     |  ||  ||||| | ||  ||||| || | | | |        | ||| |   ||
TGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatttgtaatttgtaaatgtatagtttacccatctgatcaaggccttattaacaaatatttttctaaatttcag
















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|60354743|gb|DN221716.1|DN221716
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|166443326|gb|EG172666.1|EG172666
EST:     CTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTCGCTAAAGTCCTGCAATCACTTGTACC
genomic: CTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|60356763|gb|DN223736.1|DN223736
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTATTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|149079804|gb|EE168801.2|EE168801
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|4681251|gb|AI629921.1|AI629921
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|18661338|gb|BM501361.1|BM501361
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTCGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|50336585|gb|CO531711.1|CO531711
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|7227754|gb|AW566395.1|AW566395
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTCGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|60399443|gb|DN232255.1|DN232255
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|50336586|gb|CO531712.1|CO531712
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|40303113|gb|CK347500.1|CK347500
EST:     ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAG                         GGTTCCGAACATGAAATTCAATGTCGCTAAAGTCCTGCAATCACTTGTACC
genomic: ATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC
EST: gi|116814772|gb|EC857388.1|EC857388
EST:     TTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACA-                         GGTT-CGAACATGAAATTCAATGTTGCTAAAGT-CTGCAATCACTTGTACC
genomic: TTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACC

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), 47 (downstream exon)
Score: 249

TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 161

TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 146

TGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCCAACAGTTGCTCCCTGTCGTCATTGCTTCTTCAAAGGACAGgtgagtccaa ... taattgctagGGTTCCGAACATGAAATTCAATGTTGCTAAAGTCCTGCAATCACTTGTACCAATCCTTGACCAATCT