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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttactattttgaactgctagaatggtctttactctttttgctaccctaattatatttgttggtacagttctctgtgtttatgtagtgcaccagttgaaaagtgctcattcaatattgtttaattactaaacactggaatatgccattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA

Basic information

species Zea mays
transcript GRMZM2G017077_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017077_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g67000.1 (Oryza sativa), 3'ss of exon 6
--------gtgagttactattttgaactgctagaatg--gtctttactctttttgctaccctaattatatttgttggtacagttctctgtgtttatgtagtgcac----cagt----tgaaaagtgctcattcaatattgtt----taattactaaacactggaatatgccattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA
         | || | | | ||| ||||||| | |||   | || || || |    ||     ||||||     |  || | || ||||   | || ||  |||     || |    || | ||| |  |||  ||| | ||    ||||| |||     ||||||||||||| |||||| ||||||| ||||||||||||||||| ||||| ||||| |||||| ||||||| |||||||||||||| ||
gtgagcttattagcttcaagtttcaactgctgggatgctattttcacactctgcattatatgtattataacgaatt-tatatttatctggcctcatatatggcatagagcaatagagtgtatagtacctatttcatactattcaactaattgctatcatgtggaatatgccatcctgtagGTTCTTGAAAGCAAGATAGCAGAGGCTAAGCAAAAAAAAGATACCTTAAAAGCCCGTGCTCAATCAGCCAA
















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|148944869|gb|EC890024.2|EC890024
EST:     AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATATCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|211105622|gb|FL311199.1|FL311199
EST:     AGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: AGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|148944166|gb|EC889255.2|EC889255
EST:     GCTTGATCAGCAGAAGGGTGTAGTTG-AAATACTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: GCTTGATCAGCAGAAGGGTGTAGTTGAAAAT-CTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|18649725|gb|BM498544.1|BM498544
EST:     AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATATCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|211491331|gb|FK964770.1|FK964770
EST:     CTTGATCAGCAGAAAGGGTGTNAGTTGAAAATCTGATTTCAAATACCCGG                         G
genomic: CTTGATCAGCAGAA-GGGTGT-AGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtag-
EST: gi|211491331|gb|FK964770.1|FK964770
EST:     CTTGATCAGCAGAAAGGGTGTNAGTTGAAAATCTGATTTCAAATACCCGG                         G
genomic: CTTGATCAGCAGAA-GGGTGT-AGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtag-
EST: gi|32840773|gb|CD980454.1|CD980454
EST:     GGGTGTAGTTGAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAAGATACCCTAAAA
genomic: GGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|76932094|gb|DV172939.1|DV172939
EST:     GCTTGATCAGCAGAAGGGTGTAG-TGAAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: GCTTGATCAGCAGAAGGGTGTAGTTG-AAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
EST: gi|148950083|gb|EC895617.2|EC895617
EST:     AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGG                         CTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA
genomic: AGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAA

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), 48 (downstream exon)
Score: 95

GACAATGCAAGCTCCTTAAGATCCCAGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GACAATGCAAGCTCCTTAAGATCCCAGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GACAATGCAAGCTCCTTAAGATCCCAGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GACAATGCAAGCTCCTTAAGATCCCAGCTTGATCAGCAGAAGGGTGTAGTTGAAAATCTGATTTCAAATACCCGGgtgagttact ... cattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgctcattcaatattgtttaattactaaacactggaatatgccattctgtagCTTCTTGAGAGCAAGATAGCAGAGGCCAAGCAGAAAAAGGATACCCTAAAAGCTCGTGCTCAATCAGCAAA
                         tactaaa  putative branch site (score: 130)
                                            ccattct  putative PPT
        attcaatattgtttaa  TA-rich tract