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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatactgccgtttcttttttaagcatttcaaactgtagttcctgatccagcaattgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 15
----------gtgaaatactgccgtttcttttttaagcatttcaaactgtagttcctgatccagcaattgaa-taacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG
          | |||||  |||| | | | ||| || || |||||  | |  || |||||   |||| |||  | |||||||| ||| ||||||||||| | ||||||||| |  || ||| | |||||||||||||||||||
gtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgatt--gcaaatgatcttacagCTAGCACTCGACCAACGGGAGCCTGATGATCCAAGTCCTTACCTGTTGGCCATATGGACACCAG
















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|32945243|gb|CF050062.1|CF050062
EST:     GTATGAGCTTCCAGATGCACATCCACTTTTACAACAG                         CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
genomic: GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
EST: gi|211540330|gb|FL320588.1|FL320588
EST:     GTATGAGCTTCCAGATGCACATCCACTTTTACAACAG                         CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
genomic: GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
EST: gi|67026937|gb|CO455686.1|CO455686
EST:     GTATGAGCTTCCAGATGCACATCCACTTTTACA-CAG                         CTAGGACTTGAC-AACGGGAACATGATGATCCTACCCCCATACT
genomic: GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCC-ATACT
EST: gi|60339031|gb|DN206004.1|DN206004
EST:     GTATGAGCTTCCAGATGCACATCCACTTTTACAACAG                         CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
genomic: GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
EST: gi|5901234|gb|AW042334.1|AW042334
EST:     CAGATGCACATCCACTTTTACAACAG                         CTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC
genomic: CAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCC

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), 49 (downstream exon)
Score: 343

GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 34

GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

GTATGAGCTTCCAGATGCACATCCACTTTTACAACAGgtgaaatact ... tgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttttttaagcatttcaaactgtagttcctgatccagcaattgaataacagCTAGGACTTGACCAACGGGAACATGATGATCCTACCCCATACTTATTGGCCATATGGACACCAG
                              tcctgat  putative branch site (score: 65)
     ttttttaagcattt  TA-rich tract