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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctctcctggctgtagttaatgcatttattgtgcaataaatcttggttatgattttttatcaacatgttttatgtgctattctggttgaatgtccatctgcagtattaaataccatgtctttttcttttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 11
-------------------------gtacctctcctggctgtagttaatgcatttattgtgcaataaatcttggttatga------------ttttttatcaacatgttttatgtgctattctggttgaatgtccatct----gcagtattaaataccatgtctt----------------tttcttttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
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gtgtctcttctaattcctcatcagttttgctgtcctttcactgcctcatgcatttgctctgtgctatgactggtttatgaactaaaacgatttgtattgcccaaattgggcacattctatcctgattttgtatacattcttgattaataccaaatatcatatgtcccatgtattgatcttgttcccttttctttcagGAGTTCACTTTTAAGTGTTTATGCGGACATGTCAGTAACTTGCAAG
















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|211500355|gb|FL431278.1|FL431278
EST:     GACAGAAAACTGAACAACACATATG-CCCCCTTCTTTTCAGCAG                         GAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
genomic: GACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
EST: gi|211323425|gb|FL039625.1|FL039625
EST:     GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG                         GAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
genomic: GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
EST: gi|13558607|gb|BG549963.1|BG549963
EST:     GTTTTGTCTTGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG                         GAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
genomic: G-TTTGAC-AGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
EST: gi|71765382|gb|DR963319.1|DR963319
EST:     AAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG                         GAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
genomic: AAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
EST: gi|31350094|gb|CD434451.1|CD434451
EST:     GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG                         GAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
genomic: GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG

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: 47 (upstream exon), 46 (downstream exon)
Score: 80

GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 205

GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 154

GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 82

GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcc ... ttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgaatgtccatctgcagtattaaataccatgtctttttcttttcttttcagGAGTTCACTTTTAAGTGTCTATGCAGACATGTCAGTAACCTGCAAG
                            taccatgtctttttct  CT-rich tract
 tttttcttttctttt  TA-rich tract