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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgctaagccctgcttctgtctgatactttcattagattagaatttttgttacatgctttacaagtcaatttccaaatgccatgtgaagcattagtcattgttcgtatactttttatgttaaaacatcattgtccgtttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 3'ss of exon 10
gcatgctaagccctgcttctgtctgatactttcattagattagaatttttgttacatgctttacaagtcaatttccaaatgccatgtgaagcattagtcattgttcgtatactttttatgttaaaacatcattgtccgtttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG
         ||   ||  || | |||||  |  |   || || |   || |||  ||  ||      | ||||||  |   | |    |||   | ||  || |  ||  | | | ||            | ||   ||| |||| ||||   | | || ||  ||||||| ||||||||||||||||||||||| ||  |||||||||||||||
---------gcatggcacctatgtgatatgtctacatgactaaa---ttagttttataatt-----ataaatttctgaggacaa----aagtgat-gtatttttgtgtccagtctcta------------actgcttgttcttgccagGTGGTATTCTCCCTATTGGTTGTGAGCATCCTTAGTTCCATGTCTTCGCAATCTGCATTTAAAATAG
















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|149072463|gb|EE160739.2|EE160739
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|211480846|gb|FL457134.1|FL457134
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|18450804|gb|BM429082.1|BM429082
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|32836792|gb|CD976470.1|CD976470
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|18650185|gb|BM499004.1|BM499004
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCTATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|37381967|gb|CF627894.1|CF627894
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|60337162|gb|DN204135.1|DN204135
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGT
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGT
EST: gi|32846686|gb|CD986367.1|CD986367
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|31364078|gb|CD448433.1|CD448433
EST:     GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
EST: gi|32809804|gb|CD962038.1|CD962038
EST:     GATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAG                         GTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG
genomic: GATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAG

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: 45 (upstream exon), 48 (downstream exon)
Score: 112

GGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCTTTAGTCAGTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 49

GGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCTTTAGTCAGTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 59

GGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCTTTAGTCAGTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 54

GGCTCATCATATTGCTAATTCCATTAGTTCGAATTGGAACTCTTTAGTCAGTGCGCTAAGATCTCTTTGTAGAGGAAATGATTGGCTATTGTTTCTCAAGgcatgctaag ... tttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtcattgttcgtatactttttatgttaaaacatcattgtccgtttttgctagGTTTCACTATCTCTGCTGGTTGTCAGCATCCTTAGTTCCATGTCTTCTCAGGCTGCATTTAAAATAG
                                         tccgttttt  CT-rich tract
              tatactttttatgtta  TA-rich tract