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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaactgaattaatatttagattaaattgctagtatgttcatatagttattttttcctttgctgttttatatattttttgggtctgttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG

Basic information

species Zea mays
transcript GRMZM2G406603_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406603_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 5
gtaagtaac-tgaattaatatttagattaaa--ttgctagtatgttcatatagttattttttcctttgctgttttatatattttttgggtctgttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG-------------------------------
||||||    || | | |||   |||||| |  || | |||||    | ||    || |||| ||||  | ||||| || || ||  |     |    ||||||| || ||||| || |||||||| ||||||||||| ||||| ||||||||||| | |||||| || |||                               
gtaagttttgtggaattataca-agattacagtttacaagtatacaaa-atgtgcatgtttttctttcattttttacatcttcttctgtctcata--atgcagCCACGATGGGCCGACCTTGATATCAATCAGCATGTTAATAACGTTAAATACATAGGGTGGATCCTAGAGGTAAAAAAAGTTCCCCTATTATGTTCATCTT

upper sequence: GRMZM2G406603_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G08060.2 (Glycine max), 3'ss of exon 4
gtaagt-aactgaattaatatttagattaaattgctagtatgttcatatag-ttattt----tttcctttgctgttttatatattttttgggtctgttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG
||| || ||||   ||  | | ||  |    |   || | | ||     |  ||||||    | |  ||| ||  ||  | ||  |  ||  |||   || |||||||| | |||  |||||| ||||| |||||||||||||| ||||| || |||||||  |||||||| |||
gtatgtcaactagttttttttctaattgctgtcattaatttattttctcaaattatttcagatgttgttttctaattagtttacataatgcatcttcattttgcagCCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG

upper sequence: GRMZM2G406603_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G12940.2 (Glycine max), 3'ss of exon 5
gtaagtaactgaattaatatttagattaaattgctagtatgttcatatag-ttattt----tttcctttgctgttttatatattttttgggtctgt-tttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG
||| || |   | ||  | | ||  |    |   || | | ||    ||  ||||||    | |   || ||  ||  | ||  || ||  |||   ||  | ||| || | |||  |||||| ||||| |||||||||||||| ||||| || |||||||  |||||||| |||
gtatgtcaactagtttttttgtaattgttgtcattaatttcttttcttaaattatttcagatgttgctttctaattagtttacattatgtatcttcattcttccagTCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGACTGGATTCTGGAG

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|32869619|gb|CF009301.1|CF009301
EST:     CAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACT                         CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
genomic: CAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
EST: gi|24773338|gb|CA408592.1|CA408592
EST:     CAGAGGGACAAAGCACTTCTGTAGCTAAATATGTGAGGACAGGCCTGACT                         CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
genomic: CAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
EST: gi|24961561|gb|CA483567.1|CA483567
EST:     TATGTGAGGACAGGCCTGACT                         CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGCTAAATAC
genomic: TATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
EST: gi|60356288|gb|DN223261.1|DN223261
EST:     CAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACT                         CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC
genomic: CAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATAC

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), 48 (downstream exon)
Score: 87

TGAGCATTCTGCTATTGTTGACGAAGACAACCGCAAGCTTCCAAAACTGCCAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 121

TGAGCATTCTGCTATTGTTGACGAAGACAACCGCAAGCTTCCAAAACTGCCAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 81

TGAGCATTCTGCTATTGTTGACGAAGACAACCGCAAGCTTCCAAAACTGCCAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

TGAGCATTCTGCTATTGTTGACGAAGACAACCGCAAGCTTCCAAAACTGCCAGAGGGACAAAGCACGTCTGTAGCTAAATATGTGAGGACAGGCCTGACTgtaagtaact ... ttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagttattttttcctttgctgttttatatattttttgggtctgttttgtgcagCCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG
                                         tctgtttt  CT-rich tract
                tttgctgttttatata  TA-rich tract