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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttatctatatcctttaatttcattaatgatctttcttgacacgatgtattttgtgtttgatggggttgggtcagttatttcggtactattttgcaataagtaattgatggcctattttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 3'ss of exon 7
gttcttatctatatcctttaatttcattaatgatctttcttgacacg---atgtattttgtgtt-tgatgg----ggttgggtcagttatttcgg------------tactattttgcaataagtaattga----------tggcctattttaaa-ttaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC
||  |||||| |      |||| | |||| | ||   |||||| |      ||| | | ||  | || |||           ||| | | |   |            ||||    | |   |||    | |          || || ||| |||| || |||||||| | ||||||||| ||||||| ||  ||||||| ||||| || ||||| ||||| |||||||| || ||||||||||| || ||||||||||
gtgtttatctgtgattcataatgtgattagtaatagctcttgatatatttgtgtgtgtggtactgtggtggtttatacctactcaataactctagatagtccatacctacttcccttcttgaaggttctcacacatgcaactgaccaattctaaaattcagGATGGACTTAAGAGAACAATAGAGTCATATCCCCATCTGCAAGCACAAAATCAAAGGAGCATATCAAAAGCCTCAATTTTCCTTGGCAATGGAAATC

upper sequence: GRMZM2G149224_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g29170.2 (Oryza sativa), 3'ss of exon 7
gttcttatctatatcctttaatttcattaatgatctttcttgacacg---atgtattttgtgtt-tgatggg----gttgggtcagttatttcgg------------tactattttgcaataagtaattga----------tggcctattttaaa-ttaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC---
||  |||||| |      |||| | |||| | ||   |||||| |      ||| | | ||  | || |||           ||| | | |   |            ||||    | |   |||    | |          || || ||| |||| || |||||||| | ||||||||| ||||||| ||  ||||||| ||||| || ||||| ||||| |||||||| || ||||||||||| || ||||||||||   
gtgtttatctgtgattcataatgtgattagtaatagctcttgatatatttgtgtgtgtggtactgtggtggtttatacctactcaataactctagatagtccatacctacttcccttcttgaaggttctcacacatgcaactgaccaattctaaaattcagGATGGACTTAAGAGAACAATAGAGTCATATCCCCATCTGCAAGCACAAAATCAAAGGAGCATATCAAAAGCCTCAATTTTCCTTGGCAATGGAAATCGTA
















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|87151705|gb|DY396494.1|DY396494
EST:     GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAG                         GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
genomic: GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
EST: gi|32863056|gb|CF002738.1|CF002738
EST:     GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAG                         GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
genomic: GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
EST: gi|18450805|gb|BM429083.1|BM429083
EST:     GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAG                         GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
genomic: GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
EST: gi|18450804|gb|BM429082.1|BM429082
EST:     CTCGTGTCCCTTAAG                         GATGGAGTGAAGAGACCAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
genomic: CTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
EST: gi|22489855|gb|BU049778.1|BU049778
EST:     GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAG                         GATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
genomic: GCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAAT
EST: gi|31364547|gb|CD448902.1|CD448902
EST:     CTCAAGAAGCAA-GGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTTAG                         GATGGAGTGAAGAGAACAGTAGAGTCGT
genomic: CTCAAGA-GCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGT

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: 124

GCTGACCCCTTCAAGGATCAGGCTGCTTTCATGTAACAGGACATTCAGTTGCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GCTGACCCCTTCAAGGATCAGGCTGCTTTCATGTAACAGGACATTCAGTTGCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 63

GCTGACCCCTTCAAGGATCAGGCTGCTTTCATGTAACAGGACATTCAGTTGCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

GCTGACCCCTTCAAGGATCAGGCTGCTTTCATGTAACAGGACATTCAGTTGCTCAAGAGCAAAGGAGCAGCTTGGTTATGAACCTCTCGTGTCCCTTAAGgttcttatct ... ttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttatttcggtactattttgcaataagtaattgatggcctattttaaattaagGATGGAGTGAAGAGAACAGTAGAGTCGTACTCCCATCTACAAGCTCAGAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC
                              aattgat  putative branch site (score: 93)
                                       cctatttt  putative PPT
                                         tattttaaattaa  TA-rich tract