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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttagttattgcttgattctgcacatcaattattagctaatttggtagcattggcttcacttttctattgcttcaaaggggcagtgttaaccatcttttcttttgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

Basic information

species Zea mays
transcript GRMZM2G094039_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
gtgtgttagttattgcttgattctgcacatcaattattagctaatttggtagcattggcttcacttttctattgcttcaaaggggcagtgttaaccatcttttcttttgt---------aacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
    ||  || |||| ||||||||||| ||||||| ||| | |||| ||||||    | |||| | |||| |||||  ||||| |||   || ||||||||||| ||| |         || |||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||  |||||| || | |||
----gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG

upper sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 5
---------------------------------------------------gtgtgttagttattgcttgattctgcacatcaattattagctaatttggtagcattggcttcacttttctattgcttcaaaggggcagtgttaacca---tcttttcttttgtaa----cagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
                                                   || | ||  |||    || |  |    | |      |   ||  |||  | |    ||  |    | | | ||| ||      |      |||||     |||| |  ||| | |    |||||||||||||  | || || ||||||||||| || ||||||||||| ||||| ||||| || ||||| ||| ||||  | || ||    |||
gtctgtggattattcttggccttcagtttatttctcatgtttcattcttaagtctcttgcttacaaattaaaccatggctttttccttggcctgctttctttgtccagggatgcagtgtatcttggttgtgtctgcttactttaacttctttcttgttctttatcatattcagATATGCATGAACTACGCCTAATCCACACTGACCTAAAGCCAGAAAATATACTTCTTGTTTCCTCTGAATATGTAAAGCTCCCTAGCTATAAG

upper sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtgtgttagttattgctt-----gattctgcacatcaattattag---ctaatttggtagcattgg-cttcacttttctattgcttcaaaggggca---gtgttaaccatcttttcttt-----------tgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
                                         || | ||| ||  |          |||   || |||  || || |   ||  |||| | |    || ||  || | | ||||   |    |        || |||||    ||||| ||           |  ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG

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|71432790|gb|DR813840.1|DR813840
EST:     TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCAT                         ATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
genomic: TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
EST: gi|26559327|gb|CA831562.1|CA831562
EST:     TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCAT                         ATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC
genomic: TGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgttagt ... tttgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttttctattgcttcaaaggggcagtgttaaccatcttttcttttgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG
                            tgttaac  putative branch site (score: 2)
                                  ccatcttttcttttgt  CT-rich tract
                                       ttttctttt  TA-rich tract