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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT

Basic information

species Zea mays
transcript GRMZM2G081848_T05
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 5
-cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtat--cagtgttctgtggcgtatataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
  ||            |   ||||    | || ||||| | ||| ||||||||||   | |||||| ||| || |   | |||| |||||||  ||| ||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| |||||| |||||||||| |
atatacttcttgtgcacaatgctgaaatc-ctgaagcaccatttcatttgagtatagtattgttctatggtgtctg--atttgaatccttaattagctatcagATGACAAACACAATTCAGAAGAAATTCAAGGTATCTTCAACACAGCTGCTGTACCAATCATGCCCATACCAAGCATTGACCTTGTTCATCGTCGGCCCTT

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagcca---tcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
  | |  |  || |    |  ||   ||  |     |  | |    | ||  |   ||||  | | |  | |||   || ||  |||||  || |    ||||||||||||||| || ||||||||||| ||||| ||||| || || ||  |||| ||| | || ||||| ||| ||   || |||||  || | || ||||
tgtgactactaagaaaaagattgtccccttttttttatgcatgg--tggatcaattgtgtatttttgtct-tatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaag---ccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
 |||  |    |||||         |    |         ||| |||   |    |   || | |    | |     | | ||||||||| ||   |  | ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| ||||| || ||||| ||||||   ||  ||||  |||  || ||||
tattgcacttgaaagctttataaaggtggttgtctgcttttttcattcctgggctatcatttttt---atttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagccatc---agATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
 |||  |    |||||    |    |   ||         ||| |||   |    |   || | |  | |      |||  ||||||||  ||   |    ||||||||||||| || |||||||||| |||||| ||||| || ||||| ||||| ||||| || ||||| ||||||   ||  ||||  |    |||||||
tattgcacttgaaagctttacaaaggtggctgtctgcttttttcattcctgggctatcattttttatc-tgggcgtctt--gtccttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
-cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgt--ggcgtatataac-ttgagtccttaacaagccat---cagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
  ||   |     |  |   | |  |  || |     |  |||| |  |   |||   | || | |    |  ||   |   ||    |||||| |    |   |||||||||||||| || |||||||||||||| || || || || ||||| ||||| || || |||||||| |||||| | ||| | ||| ||   || ||||
gtatcctatgcctagcctttggt-ttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT

upper sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
------cattaaaaaaaaaagcggggctgctgccactaaagca-gcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
      |||| |              ||  | || |||  ||  | ||||   ||  |||  | ||||  ||   || ||  |  | | ||  |      |  | ||||||| ||||| || ||||||||||||||||| ||||| || || || ||||| ||||| || || || |||||| ||||  ||||| ||   |||||||
aggctgcatttatgtgtttca-ataactatttcctctagggcctgtctttgtgtt--gtaataatgtttagtcttgtttaagatcttaatcagttc----cttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT

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|148960883|gb|EE011564.2|EE011564
EST:     GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATC                         ATGACNAATACAATAC
genomic: GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATAC
EST: gi|31358400|gb|CD442757.1|CD442757
EST:     GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATC                         ATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTG
genomic: GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTG
EST: gi|148995261|gb|EE034502.2|EE034502
EST:     GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATC                         ATGACAAAATACA-TACAGAAGAGGTTCAAGGTATCTTCGACACAGCTCCT
genomic: GATCTGTATTGTCCCTACTGGCAATCATCACAACCTGCATTGCTCAGATCgtatcctttt ... aagccatcagATGACAAA-TACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
                                    gtccttaac  putative branch site 
                        tatataactt  TA-rich tract