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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 17
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 17
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                           | |  || |  | |   || |  |  | ||   |    |  ||   ||  |  |   |  ||     ||    | ||| ||   | || ||||||||||| || || || ||||||||||||||| |||| ||||||||| | || ||||| ||||||||||||
------------------------------------------gtgtttaactaatttcctttgcacaactattatgtttgccgctt--ttagtacataccttaattaatgga---gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgatttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattt--tttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                       || ||     | |||||  | ||    || |   | ||  |    |     |     | |||| || ||    ||  | || |  ||||| ||  |    |||||| ||||| ||||| ||||| |||||||| |||||||||||| | |||||||| || || || |||
---------------------------------------ttacttccagaatgttagct-ttttaaatatacgcaatgctgttgtctttcacatcttgtttacat-tggtagcaagtaatgtggtttgtgtatat-tggcagTGCTGCTGTCTTTCACAATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
lower sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgat-ttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                   | |||   |  ||   | |  |||| |  | ||  ||||||   |||  |||     ||   || ||  | |  |  | | |  | |  ||| || | |    |||||||||||| ||||||||||| || ||  | |||| ||||||  | ||||||||||| |||||||||
----------------------------------taccttcattgcgctc-tctcttttgcttgtaatactgttcg--tattgtattcaggctgtcattgttgtaac--attaaataatactgcttgcttcatt--tgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG

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|6022040|gb|AW066983.1|AW066983
EST:     TCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCNCAAGGTTTTGTGATGGGACGCGTTT
genomic: TCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     ATCACAACTGATAAAAGTGCTGCAAAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|60344250|gb|DN211223.1|DN211223
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     ATCACAACTGATAGAAGTGCTGCGGAGGCCTTTCTGCAGCAAGTTGATAG                         TGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT
genomic: ATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTT

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: 48 (upstream exon), 44 (downstream exon)
Score: 69

TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 4

TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG


Block sizes: 39 (upstream exon), 32 (downstream exon)
Score: 3

TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 294

TGCACACACAGACTGCATCATCACAACTGATAGAAGTGCTGCAGAGGCCTTTCTGCAGCAAGTTGATAGgtactgaaac ... actgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG
                                        gtttaac  putative branch site (score: 294)
                              atcattttttgtttaa  TA-rich tract