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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcgtgaaaccccccctgtttgaaggctgcttttgcaatccaccgatgtttactgacacccctaagatacttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT

Basic information

species Zea mays
transcript GRMZM2G023715_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023715_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g21230.1 (Oryza sativa), 3'ss of exon 7
gtgagctcgtgaaaccccccctgtttgaaggctgcttttgcaatccacc----gatgtttactgacacccctaagatacttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT
|| || || |||   ||  | | |||||    |   || ||||| || |     | ||  ||| ||||   || ||   |||| ||||||| || |||||||||| |||||| || |||||||| |||||||||||| |||||| |||||| ||||||||
gtaagttcctgacctcctgcttctttga---ttcagttggcaattcagctaaaaaggtgaactaacacgt-taggagttttgatgcagGCTTTTTGATGGAAACAAATTCACTGGTAATATCCCAGACTCTCTTGGGCTTGTTACTACACTTGAAGTTGT
















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|148933999|gb|EC878000.2|EC878000
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
EST: gi|76291830|gb|DV031398.1|DV031398
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
EST: gi|148981984|gb|EE028044.2|EE028044
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTTGGGT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTT-GGGT
EST: gi|71768120|gb|DR966057.1|DR966057
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
EST: gi|148981983|gb|EE028043.2|EE028043
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT
EST: gi|76291831|gb|DV031399.1|DV031399
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGAAATATCC-GGACTCTCTTGGGT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAA-TATCCCGGACTCTCTTGGGT
EST: gi|71768121|gb|DR966058.1|DR966058
EST:     GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTT                         GCTCTTCGATGGAAACAGATTCACCGGGGATATCCCGGACTCTCTTGGGTT
genomic: GGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTT

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: 39 (upstream exon), 45 (downstream exon)
Score: 8

TCACTTCAACAAGAACCAGTTGTCTGGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 73

TCACTTCAACAAGAACCAGTTGTCTGGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

TCACTTCAACAAGAACCAGTTGTCTGGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 29

TCACTTCAACAAGAACCAGTTGTCTGGTCCGATCCCCGACGCTCTCTTCAGCCCGGAGATGGCCTTGATCCACTTgtgagctcgt ... cttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctgcttttgcaatccaccgatgtttactgacacccctaagatacttgacgcagGCTCTTCGATGGAAACAGATTCACCGGGAATATCCCGGACTCTCTTGGGTTTGTTAGTACACTCGAAGTTGT
                     atgttta  TA-rich tract