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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

Basic information

species Zea mays
transcript GRMZM2G124886_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaa---aacatgtttctttgt--gtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|| |   | |||||| |   |||     |||  ||||||| | |    | |||||| ||| || ||   || ||    |  || ||  || |  ||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
gtgagtaattttgttcctggatt----taaatttttttttgcgt----gtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaa-----catgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|| |   | ||||||     ||   ||||||  | ||||      | || |||||| ||| || ||   || || |     |   ||  | | |||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
gtgagtaattttgtt----catggattcaaatttattttg-----cgtgtcatttggaatattatgatgctaaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|||| | | |||| |    |   |||| |    | |  |    | | |   |||     | |  |   | |       |  |  | |||  |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaa-gtactttgattaggtgacattt-agttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtaatggaatttgttacct--tattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
||||  |  |   | |  |   || |  |     ||||| || | ||| | |  |||    ||||       | ||||    |||  |||||| |||| || ||||||||||| ||||||||| |||| || ||||| |||||||| |||||||| ||  |||| || |||
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttc-ttcttactgtttct--tgttaattttgttaaaa----ttttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
     | || |  || | | |    |   | |   ||| | | || ||  | | | |    || |     |    | || ||||||     |||| || ||||||||||| || ||||||||||| || ||||| |||||||| |||||||| ||  | || || |||
-----gtaagtgcttgcatga--ggtggcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaat-gttgtgccactcaaaaca--tgtttct-ttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
         |  ||    | ||||  | | | ||  || |    || |  | ||   | | |||||   | | ||      | ||| | |||||| |||| || ||||||||||||||||||||| ||||||||||||| |||||||| |||||||||||| |||| || |||
--------gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------------------------------------------------------------gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgta--------gAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                                                                              ||  || ||  ||| || |  | || ||||        | |||  | |   | |     || |  ||||   ||| | ||| ||| |  |        ||||||||| ||||| |||||||||||| ||||  ||||||| |||||||| |||||||||||  | || |  |||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctga--aatttaaacgcaaaagcagattggtactgctcgc----ttat-tcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------------------------gtaatggaatttgttacctta----ttatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                                            || |||||  |  || | |     | | ||  |   |||  |    |   |    | | |  ||| |||   ||    ||||     ||   | ||||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgct----acataacgttt---gcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
---------------------gtaatg-gaatttg----ttaccttattatttcaaacctttttttacattca--tgccatttgaaatgttgtgccactcaaaacatgt-----ttctttg---------------tgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                     ||  || ||| ||     | | |   || || |||  || |  |||||||    |  || |||||| ||||| ||| | |     | |      |||||                || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaa-gttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
----gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
    ||  |  ||    |||| | |  ||| | |   |||    |||   |  | |      ||  |      ||         ||   |  |  |||||||||| |||||||| ||||||||||||||  |||||||||||||| | ||||| ||||| || || || |||
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaacta------atagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|31355222|gb|CD439579.1|CD439579
EST:     ATGATTGGGTGGAATGCAGATTGATACGCCGAATTGATGTCAATGTGAAG                         AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG
genomic: ATGATTGGGTGGAATGCAGATTGATACGTCGAATTGATGTCAATGTGAAGgtaatggaat ... ctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                        tgtttcttt  CT-rich tract
             atttgaaat  TA-rich tract