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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcataaactacctttttagtgcaccttttctattatttggtaacttttggtgtgtatctagcattatattgctttatactgatttttccttgtacatgatttgtgtagtaggtagattatattatgaaactgctgctggcaggtttctaataagctggtttttttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG

Basic information

species Zea mays
transcript GRMZM2G013283_T01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 26
gtcataaa--ctacctt------tttagtgcaccttttctat--------tatttggtaacttttggtgtgtatctagcattata--ttgctttatactgatttttccttgtacatgatttgtgtagtaggt-agattatattatgaaa------ctgctgctggcaggtttctaataagctggtttttttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG
||||||||   ||  |       |  | | ||  |||   |          ||||| ||  |  |  ||||||  ||| || ||   || ||||||| |    |    |   |     ||||     || || ||  | ||  | ||||      |  | | |   ||||||    |||  ||   |||| |||| |||||||| | || |||||| | ||||||||||| ||||||||||||||| ||||| |||||| | ||| ||||
gtcataaaacttatttcatctactcgaatacaattttgtgacattagatacatttgttacgtgctcatgtgtacttagtatcatgtgttcctttatattagactactatcagagtaattttgcagtatatgtcagcctgtaaaaagaaaaaagaacatcagttccaaggttttc--taatatgtgattttcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG
















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|12046201|gb|BF728340.1|BF728340
EST:     ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAG                         AATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
genomic: ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
EST: gi|14191259|gb|BG833489.1|BG833489
EST:     AATTGCATACGACAAA-GGTCCCGCATACTGCTACAG                         AATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
genomic: AATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
EST: gi|78180848|gb|DV551221.1|DV551221
EST:     ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAG                         AATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
genomic: ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
EST: gi|6827611|gb|AW331254.1|AW331254
EST:     ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAG                         AATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT
genomic: ACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGT

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), 41 (downstream exon)
Score: 33

TGAGAACCTTGATGGATCTAGTTCTGTAACAGATAATAAACAATCCGATCACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 24

TGAGAACCTTGATGGATCTAGTTCTGTAACAGATAATAAACAATCCGATCACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

TGAGAACCTTGATGGATCTAGTTCTGTAACAGATAATAAACAATCCGATCACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG


Block sizes: 28 (upstream exon), 41 (downstream exon)
Score: 14

TGAGAACCTTGATGGATCTAGTTCTGTAACAGATAATAAACAATCCGATCACCTGCTAATGGTAATTGCATACGACAAATGGTCCCGCATACTGCTACAGgtcataaact ... ttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattatgaaactgctgctggcaggtttctaataagctggtttttttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG
                                        ttttttt  CT-rich tract
                                        tttttttaatttca  TA-rich tract