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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataactaccttcttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG

Basic information

species Zea mays
transcript GRMZM2G384439_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g07760.1 (Oryza sativa), 3'ss of exon 7
--------------------------------aataactacctt--cttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgaca-------tcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---
                                |   |  ||  |   ||||||||||  |      || |     |     |  |   | ||||||||||||| | | |  | ||||||        || || || |  ||| |||   || || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||| ||||||| |  |  |||||   
gtgagatctgttcatattcacagctgtgcaacagccaacactatgatttttttttgttgcactgacgcgtggtacttatgctggtatggactatggaacatattgttgttgttctgacaataataacctcatgttctatagGGAGT---TCATCTAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGAGCAGCCTTGCTATTTGCTATTCCTGCTATTGGTTTTGCATGGTATCGGCGCAG

upper sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------aataactaccttcttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---
                                      |  |  |  |  ||  || | |  | | |||   ||   ||   | | ||   | | ||    || ||  |    | |   | || | ||||        | || | | |   |  ||||||||||| ||||||||||| ||||| ||||| || ||||| ||||||  |||||||||    ||||| |  ||||| ||   
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcct-ttttctcatataactcatcttgccaataaggca-ataaccaaatgatcta-atttgatttc-------agGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG

upper sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 7
aataactaccttctt-ttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---
  | | |   |  ||  |||||||    | ||   |||  |||     | |     ||  | ||  ||     | | |   |    ||  || |  | ||||| | |    | |||   | |||||||||||||| ||||||||||||||||| || || || ||||||   || |||||| ||||||| |  ||||||||   
-gtgattggataattgctttttgttgaaatccaaaatttctattattttcagatctgcactagaggattaaattatttgtttcttttcaaatgtcattcagGAGGAAATAGTGCCA---CAGGAGCAATTGCTGGAGGAGTGGCTGCTGGTGCTGCTTTACTGTTTGCTGCACCAGCAATTGGTTTTGCATGGTGGCGGCGGAG

upper sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 7
aataactaccttcttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttatttt---ttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---
|  ||  |       |  ||| ||       |     || ||     | |  |  | |||    | |   |  || || || |  |||  ||     || ||||| | | |  | |||   | |||||||||||||| || |||||||||||||| || || |||||||||  |||||||||| ||||||| |  ||||| ||   
agaaaagaaaaagactggtttctcttacagttatgacagcattct--ttagaagagttatcatccttgcaggattatt-ctaatctctctttcaacatttcagGAGGGAACAGTGCCA---CAGGAGCAATTGCTGGGGGTGTGGCTGCTGGTGCTGCTTTACTATTTGCTGCTCCTGCAATTGGTTTTGCATGGTGGCGCCGAAG

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|26558051|gb|CA830286.1|CA830286
EST:     CTTTTCTCCACCTCCTCCATACAACCCTACAACCCCTGTGCAATCACCAG                         GAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTG
genomic: CTTTTCTCCACCTCCTCCATACAACCCTACAACCCCTGTGCAATCACCAGgtgatttact ... ttttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaattaaggctatggaacatatggctttgttactgacatcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG
                                tactgac  putative branch site (score: 1)
                                        tcttatttttt  CT-rich tract
                                     acatcttatttttt  TA-rich tract