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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcttacttacagctaataataccatccaatcatattttcttttctttttccagctagtgtttttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA

Basic information

species Zea mays
transcript GRMZM2G477146_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G477146_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 4
-gcttcttacttacagctaataataccatccaatcatattttcttttctttttccagctagtgtt-tttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA
    |  |  || || | ||| |||   |    ||||||   ||    | || | |  ||  ||   |||| |     |||| |||| || ||   ||||||||||| ||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||||||||| |||||||||||
gtactagtgattccacccaatgatattttttt-tcatatccactccagtattgc-aattaacgtaacttggaaaaatgattgtttgtgtaattttattgcagTCACTTCTTGCAGCTCTTGGATCGATTCAATTTGTGTCCAATATTGCATTTGCTTACTTTGTGTTGAACAAGACCATTTCAGTGAA

upper sequence: GRMZM2G477146_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 4
gcttcttacttacagctaataataccatccaatcatattttcttttctttttccagctagtgtttttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA
   |   |    | |||    ||  | | |   | |  ||| |    |||    |     | | ||||||      |  | || |  |||  |||||||||| || || |||||||||||||| ||||| ||||| |||||||| || ||||| ||  |||| |||||||| |   || | || ||
--gtagaatgatctgctcgacattgcctacttgcgtgatttgtcaggtttcattatggtttctctttggttttcttaccg-ttatgaactctctttgcagTCCCTTCTAGCAGCTCTTGGATCCATTCAATTTGTATCCAACATAGCATTTGCTTATGTTGTATTGAACAAAATGGTTACTGTCAA

upper sequence: GRMZM2G477146_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 4
gcttcttacttacagctaataataccatccaatcatattt--tcttttctttttccagctagtgtttttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA
| |  ||   |     | ||  | |  | |  ||  ||||  | ||| |||| ||  ||   ||  ||   | |     ||  ||  ||   |||| |||||||||| |||||||| || ||||||||||| || |||||||||||||| ||||||||||| || |||||||| |   | || || ||
gatggttggatgacattgatttttcttttctttctaatttattttttcctttctcttgcctttggcttcctttcccc--ttcttttcttttatgctgtgcagTCACTTCTTGCAGCCCTGGGATCAATTCAATTCGTTTCCAACATTGCATTTGCCTACTTCGTTTTGAACAAAATGGTGTCTGTCAA

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|78106037|gb|DV524455.1|DV524455
EST:     TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAG                         TCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
genomic: TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAGgttcgtttcg ... tgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
EST: gi|67033412|gb|CO462161.1|CO462161
EST:     TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAG                         TCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
genomic: TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAGgttcgtttcg ... tgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
EST: gi|76918522|gb|DV167332.1|DV167332
EST:     TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAG                         TCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
genomic: TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAGgttcgtttcg ... tgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
EST: gi|71332502|gb|DR803214.1|DR803214
EST:     TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAG                         TCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT
genomic: TTGCTGCTGGGAACTGCCTCAATTTCATGTCATTTGCGTATGCTGCACAGgttcgtttcg ... tgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttccagctagtgtttttggtacggaaattgattgtttacttgctttgcagTCACTGCTTGCAGCTCTTGGATCAATTCAGTTTGTTTCCAACATTGCTTTTGCCTACTTTGTGTTGAACAAGACTATTTCAGTGAA
                              aattgat  putative branch site (score: 4)
                                           cttgcttt  putative PPT
                             aaattgattgttta  TA-rich tract