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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA

Basic information

species Zea mays
transcript GRMZM2G027851_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                         ||  ||  | | | | |  | | ||||  ||| |  ||||||   |  | |  |||           |||||| | | ||   |   |||||||||||| ||||||||||||| |||||| |||||||||| || |||||||| || || ||||||||||| || ||  ||||||| ||||||||||| ||||
----------------------------------------gttagttgaacaaattttgccatacctc--gagagagacctggattcaacgtgctaa-----------tgtaatgatc-ttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 5
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                             |||| |||  ||| |      |    |  | | |   |   |      || |||  |  |  ||| | | |  | |    | |   ||||| ||  | ||||||||||| || || ||||||||||| || || || ||||| || ||||| ||||| || ||||||||||| || || ||| |  | |
--------------------------------------------gtttggaacgatatgtgcctttttcgcaatgtagc--agcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttg---cagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTTGTGCTTTTTAATGCAATAAAAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgagggga----acctggtccctgcttagtaaattatttgacctgtaatcaccattttactg-gaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                                     | | |   | |||  ||    | |    |    | ||| |  |   |   || || ||    | ||    |  |   | || |||||| ||| |||| |||||||| || || || |||||||| || || || ||||| || ||||| |||||||| ||||||||||||||||| ||  | ||||
---------------------------------------------------gtaatgtgattcgccaattagcagaagtacatacaggcccagaatcaaagtgtaattaacaaaaactcttgttcctttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
gttggttggttggttggttgctggaacaatctcatggacatttcatt-tgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                  |  | ||  | ||   || | ||  ||| ||   ||  ||    |   |    |   |    || ||||||  ||   |||| | ||| |        ||||| ||  ||||||||||||| ||||| || |||||||| || || || || || || ||||| |||||||| ||||| ||||| ||||| ||| ||||||
---------------------------------gtacagatggccttactaagctgtg-atcctgttact--agttctaagggacaacacttccacaacttatttatcc---aatc-caattgtg-------cagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

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|74239375|gb|DT647289.1|DT647289
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|50333105|gb|CO528231.1|CO528231
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|78080130|gb|DV508542.1|DV508542
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|74238599|gb|DT646513.1|DT646513
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|93282181|gb|EB674445.1|EB674445
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|78093453|gb|DV521827.1|DV521827
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|78115473|gb|DV533861.1|DV533861
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                     atttgac  putative branch site (score: 4)
                                        ttttact  putative PPT
           ttagtaaattatttga  TA-rich tract