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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgtttttttacagtttcaataaaaatattattatgttaattattaagttagtacctgtaattctttctgattttagcagtactaaattctgttttccaattctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 13
gtaagct-gttttt-ttacag------tttcaataaaaat-attattatgttaat---tattaagttagtacc------------tgtaattc--tttctgattttagca-gtactaaattctgttttccaattctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC
||||||| |||||| |||  |      | ||| |||| || | || |||| ||||   |||| | || | |              |  | |||  ||| | ||| |   |   | | |||     |||    |  | | |||| ||||||||||||||||| |||||||||||||| |||||||| ||||||||||| || |||||||| || ||| |||||||||||||||| ||||||||
gtaagcttgtttttgttattgaattcttgtcactaaatattactagtatgataatggttatttattttgcataaactaagcataatacatttcctttttttattatgatatacattgaatgaatgttttttttcttctacagACGGTATCTGCCATGTTTATATTGACAAATCAGCTGACATGGACATGGCAAAACGTATTGTATTGGACGCAAAGGTTGATTATCCAGCAGCGTGTAATGC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 13
gtaagctgtttttttacagtttcaataaaaatattattatgttaattattaagttagtacctgtaattctttctgattttagcagtactaaattctgttttccaattctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC
                                             | |   |  | ||  || |     ||| | || |    | ||     ||   | |     ||   |||||||||||| |||||||||||||| ||||| |||||  | ||| | |||||||| |  || || |||||||| ||||  |||||||| ||||| ||||||||
--------------------------------------------gtaagataaattgtgactctttaaatttataatctgcaaactagaggttttattatagtgtttgctttcagATGGTATTTGCCATGTTTACATCGACAAGTCAGCTAATATGAAAATGGCAAAGCACATTGTTTTGGATGCGAAGACCGATTATCCTGCAGCCTGTAATGC
















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|32931318|gb|CF036130.1|CF036130
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|33094388|gb|CF054382.1|CF054382
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|32931519|gb|CF036331.1|CF036331
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAGTCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     CAACAACTAAAATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: CAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|24934245|gb|CA452463.1|CA452463
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|211307860|gb|FL092738.1|FL092738
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|211307861|gb|FL092739.1|FL092739
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGAC
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGAC
EST: gi|211307862|gb|FL092740.1|FL092740
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
EST: gi|32932079|gb|CF036891.1|CF036891
EST:     AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTG                         ATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA
genomic: AGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAA

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), 47 (downstream exon)
Score: 154

CTTGATGATGTAATTGATCTTGTCATTCCGAGAGGTAGTAAGTCTCTAGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 20

CTTGATGATGTAATTGATCTTGTCATTCCGAGAGGTAGTAAGTCTCTAGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 12

CTTGATGATGTAATTGATCTTGTCATTCCGAGAGGTAGTAAGTCTCTAGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 493

CTTGATGATGTAATTGATCTTGTCATTCCGAGAGGTAGTAAGTCTCTAGTTTCCCAAATCAAAGCAACAACTAAGATTCCAGTTTTAGGTCATGCTGgtaagctgtt ... ttctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaattctttctgattttagcagtactaaattctgttttccaattctgttcagATGGTATCTGCCATGTTTACATTGACAAATCAGCCGACATGGATATGGCAAAACGGATAGTATTGGATGCTAAGATTGATTATCCAGCAGCATGTAATGC
                         tactaaa  putative branch site (score: 493)
                                             ttctgttc  putative PPT
                         tactaaatt  TA-rich tract