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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaatgccgtctctgcttctggttgctccgtttgcacttggcagtatgattatccttggcagcagggagcggcgatgtttgaattatgcatttttttctgttgagcctagatcatgactgtgctgggctcgttcaattccactgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG

Basic information

species Zea mays
transcript GRMZM2G126453_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 26
-----------gtacacaatgccgtct-ctgcttctggttgctccgtttgcacttggcagtatgattatccttggcagcagggagcggcgatgtttgaattatgcatttttttctgttgagcctagatcatgactgtgctgggctc--gttcaattccactgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG
| || ||| ||| ||| ||||| || | | | || || | ||| | | | | | | || || | || | | | |||| | |||| |||| | | | |||||||| ||| |||| ||| ||||||| ||||| ||||||||||| ||||| || |||||||| || ||||| | | ||||||| ||||||||||||||||
gttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATG
















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|32921157|gb|CF025969.1|CF025969
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
EST: gi|211048841|gb|FL187601.1|FL187601
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGG
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGG
EST: gi|211048838|gb|FL187598.1|FL187598
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
EST: gi|32921345|gb|CF026157.1|CF026157
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
EST: gi|211048837|gb|FL187597.1|FL187597
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA
genomic: TGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGA

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: 241

AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 222

AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatg ... ctgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttgagcctagatcatgactgtgctgggctcgttcaattccactgtgtgcagGAGAAGAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATG
                                        ttccact  CT-rich tract
 ttcaatt  TA-rich tract