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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 49
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttg--taatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC
|||||  |  ||| || ||  || |       ||  ||| |||         | | |||| ||| ||    |||||  |  ||||   | ||||  | |||||||||||||||||||| || ||||||||||  || ||||| |||||||||||||| || || ||||| ||| | ||||||  ||||||||||||||| || |
gtttgctatttcaatcctggaggtgt------ttaagctagtt---------ttggtgtt-tttaac---tgattggct--attatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
-------------gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatg-ttgtttgacgtacgattga---tttaattac-----attg-tttgtaa------tgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAA---TACCCAATCCAAAATTTGCACCATCCC
               |||||  || |  ||||||        || ||  || | |||  ||  ||     | |||   |  |||  |||||   ||| |  |      |||| ||| | |      ||||| ||||||||||||| |||||||||||||  ||||| ||| | ||  |  | || || || ||   | |   ||   || |   |||  | ||||||||     
gttgagttaatttacttgta--ctaacacatgttctta-attggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 22
gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaatta----cattgtttgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAA---TACCCAATCCAAAATTTGCACCATCCC
|| || |   | ||  || |       |    ||         |  ||   |||| |    ||| ||   |  ||  |||  ||     | || ||  |  ||||| ||||||||||||||||||||||||| |  || || ||  | ||  | || || || |||||     |   ||   |  |    || ||||||||||||    
gtctgca--tttaga-atatccaaattgaaaattcca------ggattacaatgggtacattttaacaagcagtttcttttcttttcctcctttttgttgttgcagATGGAGAAGAATGCAGCAGCTGGAAGGACCCCATCGAGCTTGCCCATGTCGACACCTCCCCCTTCTTCTCTAAGCCTTTCTTCCCCCAAATTTGCACCAC---

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|93014606|gb|EB640126.1|EB640126
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|20512828|gb|BQ280026.1|BQ280026
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGTATAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGG-AGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC
EST: gi|6095379|gb|AW120046.1|AW120046
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAAGA-TGCAGCAGCTGGAAGA-TGCCTTNCAGTCTTCCATTATC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAA-GAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC

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: 140

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 49

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC
                             atttaat  putative branch site (score: 160)
                             atttaattacattgtt  TA-rich tract