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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcacatgagcttgagcttcagtttcatggttctgttacttcttagttgttcagtattcatgcatgtgattgtctctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG

Basic information

species Zea mays
transcript GRMZM2G040017_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 8
gtaagtgttcacatgagcttgagcttcagtttcatggttctgttacttc--ttagttgttcagtattcatgcatgtgattgtctctc--ctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG
|||||  || | ||| |||     || |  ||  |  ||||| | ||||  ||   |  | | | |   || |  ||||||| ||||  |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||
gtaagcatttagatgtgctcagttttgatgtttct--ttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcagGACATAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTTGTG

upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtgttcacatgagcttgagcttcagtttcatggttctgttacttcttagttgttcagtattcatgcatgtgattgtctctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG
|| |||| | | | ||     |      |||   |  || || |   | ||| || | | | ||| |   |  |       ||| ||  ||||||| ||| | || ||||||||||||||||| ||||| ||| |||||||||||
gtgagtgcttagaagaatgcaaat---ggttggttttttttgct-tatgttaattctgctg-attgacctacat-------tcttctatagGACATCACAATCGGAGTTGCAATTGGTTCATCTACACAAATAGCAATGTTTGTG
















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|211272295|gb|FL440029.1|FL440029
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACMCAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|149085153|gb|EE174657.2|EE174657
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|211010290|gb|FL457993.1|FL457993
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|91868897|gb|EB400200.1|EB400200
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|32837305|gb|CD976983.1|CD976983
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|32836604|gb|CD976282.1|CD976282
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
EST: gi|148972711|gb|EE023671.2|EE023671
EST:     ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTT                         GACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT
genomic: ATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTT

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), 47 (downstream exon)
Score: 148

GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 160

GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttc ... tctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgttacttcttagttgttcagtattcatgcatgtgattgtctctcctgcagGACATAACACTGGGTGTTGCAATTGGTTCATCAACACAGATATCAATGTTTGTG
                                        ttgtctctcct  CT-rich tract
                         tattcat  TA-rich tract