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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaacttctgcttccctttaatgctattagttcgtagtttttctgtagcttagtttaattgccacttcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG

Basic information

species Zea mays
transcript GRMZM2G160460_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 12
gtaactaacttctgcttccctttaatgc-tattagttcgtagtttttctgtagcttagtttaattgccacttcaattgc-agATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG
|||| |  ||||  | |     ||| || |  || ||    || ||     | | || |  |  |  | |||||| | | |||| ||||||||||||||||||||||| || |||| ||||||| ||||||||| | |||||
gtaattctcttcctcctgaaactaaagcatgctaattttctgtattctgtgaccataataaagctctcgcttcaacttctagATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG

upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 12
gtaactaacttctgcttccctttaatgctattagttcgtagtttttctgtagct-tagtttaattgc-cacttcaa-ttgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG
     ||| |||  ||||||  | |    |    || ||   || |||||| |  ||   || |  | ||||| || |||||||| ||| ||||||||||||||||||| ||||||| |||  || |||||||||   |  ||
----gtaatttcctcttcccaatgaaatcacctttttgttagttgtctgtaacaataacatagtgactcacttaaaattgcagATCTCTACTGCTGGGATGACTCTAAGCCTTCTTGCAGTATCTGTTGTATTTTTTCTGGAG
















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|78105585|gb|DV524003.1|DV524003
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|32837362|gb|CD977040.1|CD977040
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|60400681|gb|DN233488.1|DN233488
EST:     ACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: ACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|32839330|gb|CD979011.1|CD979011
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|60350213|gb|DN217186.1|DN217186
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|32838171|gb|CD977849.1|CD977849
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
EST: gi|78121863|gb|DV540247.1|DV540247
EST:     TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATT                         ATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT
genomic: TTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTT

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), 45 (downstream exon)
Score: 28

GTTCTTGCCACTTTTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 96

GTTCTTGCCACTTTTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

GTTCTTGCCACTTTTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 38

GTTCTTGCCACTTTTGTTACAACCATGTTCTTGGACAGAGCTGGGCGGCGAATCCTCCTTATTgtaactaact ... tcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctattagttcgtagtttttctgtagcttagtttaattgccacttcaattgcagATTTCTTCTGCTGGGATGACTCTAAGTCTTCTTGTAGTTGCTATTGTATTTTACATCAAG
                               gtttaat  putative branch site (score: 38)
                                        ccacttc  putative PPT
                            ttagtttaatt  TA-rich tract