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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttttacattatttccattaccgagtacttgtagcagaacattctctataaatatagtttagctaatgcgatggggttacctgcacc...

Basic information

species Zea mays
transcript GRMZM2G051050_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051050_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 5'ss of exon 9
CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttttacattatttccattaccgagtacttgtagcagaacattctctataaatatagtttagctaatgcgatggggttacctgcacc---
|||||||||||||||||||||| ||||||||||||||||||||||| ||||||||| ||||||| ||||| ||||||||||||||||| |||||||||| |||    |||    || ||||   |      | ||||||| | | |    | |  |  ||||  |||||||| || || ||   |  |  | |   
CAAATCACCTGGATTACCTTGGTCTTCAAGTTGCATGGGTTACTGGACCATGGTTCCTATCCATTTTCACCAATGTGCTTCCTTGGGAGAGTGgttagatttttacctttgttgttctttca--tgtttgtttcttgtaggaaaccccatttttaatttataccttagctaa-gccattggtggagatataacaac

upper sequence: GRMZM2G051050_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G44110.1 (Glycine max), 5'ss of exon 9
CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttttaca--ttatttccattaccgagtacttgtagcagaacattctctataaatatagtttagcta-atgcgatggggttacctgcacc-----------------------------
| ||||| || ||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||   |||  |||||||||||||||||||| ||  ||||| || |  |   ||| |    |  || ||| |||    || ||  ||  | ||    |  |   |  |  | || || |  | | || |                                
CCAATCATCTAGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTGgtcaggttttatgttctatctatttagtagtgtagcctagt-cttacttcacaaagttgccaatgtgaaatgagcatttgtacgctattgtttgagcttccttctgatccattgtaattatttggacttcag

upper sequence: GRMZM2G051050_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G38810.1 (Glycine max), 5'ss of exon 9
CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttt-tacatt-atttccattaccgagtacttgtagcagaacattctctat---aaatata-gtttagctaatgc-gatggggttacctgc--acc-----------------------
| ||||| |||||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||   |||  |||||||||||||||||||| ||  ||||| || | |  ||| | |  | |  |  |||| |||   || ||  ||  | ||   ||||     |||    | |   | | | | | ||| |  | |                       
CCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTGgtcaggttttatgttctatctattgagtagcgtagcttagta-ttgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcag

upper sequence: GRMZM2G051050_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 5'ss of exon 9
CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttttacattatttccattaccgagtacttgtagcagaacattctctataa-atatagtttagctaatgcgatggggttacctgcacc-----------------------------------------------------------
   |||| |||||||| |||||| | ||||| || |||||||| |||||||||||  | |||||||||| |||| ||||||| |||||||||||| ||  ||||    ||   ||||   |  |        |  |  |   ||  |     || |  ||   |   | ||  |   ||  | | | ||    |                                                           
TTCATCATCTGGATTATCTTGGAGTGCAAGTGGCTTGGGTTACAGGGCCATGGTTTCTTTCCATCTTCATGAATATGCTTCCATGGGAAAGTGgtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaaatgttcgtcttcttgatcacag

upper sequence: GRMZM2G051050_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 5'ss of exon 9
CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagactttatttttttacattatttccattaccgagtacttgtagcagaacattctctataaatatagtttagctaatgcgat--ggggttacctgcacc--------------------------------------------------------------------------------------
  |||||||||||||  || ||| | || || |||||||||||||| || |||||  | ||||| || | |||| ||||||| |||||||||||| || ||  ||  |     || ||    ||||     || |||  ||  |   | |  |  |||| || ||    |  |  |||    ||  | || |||                                                                                       
TTAATCACCTGGATTTTCTGGGAGTGCAGGTGGCATGGGTTACTGGACCGTGGTTTCTTTCCATTTTTATGAATATGCTTCCATGGGAAAGTGgtcagtctccatcatggcttat-atagaaattagatgttatttggggcctacattgcatttaaaatctatttatatttctttgatttatggccatct-cactaatcttagcattctcattgtcatgattgcattcataatgtcttggttacaagcttatgggttttgatggctttctcctgacttcag

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|87152631|gb|DY397420.1|DY397420
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
EST: gi|32851391|gb|CD991072.1|CD991072
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
EST: gi|19058398|gb|BM737065.1|BM737065
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
EST: gi|22490585|gb|BU050508.1|BU050508
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
EST: gi|32851141|gb|CD990822.1|CD990822
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
EST: gi|19057887|gb|BM736554.1|BM736554
EST:     TGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTCCCTTGGGAAAGTG                         TTCTCCGTGTCTGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT
genomic: TGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGT

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), 47 (downstream exon)
Score: 126

CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGTTCCGGACAGCTCTTGCGCTACTGGAGTTCTATG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 44

CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGTTCCGGACAGCTCTTGCGCTACTGGAGTTCTATG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 68

CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGTTCCGGACAGCTCTTGCGCTACTGGAGTTCTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTGgttagacttt ... tacatttcagTTCTCCGTGTATGGGATGTGCTTTTGTTTGATGGAAACAGAGTAATGCTGTTCCGGACAGCTCTTGCGCTACTGGAGTTCTATG