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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

Basic information

species Zea mays
transcript GRMZM2G421857_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataat------------tatcaatgttttctaaaaact-----tgaaattgccaagcattttcag-atgatgtttcacttcatctt---actgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
||||||  | ||  | || ||    |   |   ||||||            |  | || |||  |||    |     |  ||   | ||    |   || |   | || | | || | ||   ||| || ||| || || |||| | | |||  ||| | |  ||||||||||| |||||| | |||||||| ||||| ||||| || ||||| ||||| ||||| ||||| ||||| || |||||||||||||||||||||||||
gtttgtacagaacctaccatggttctcactcataataatatgtgcttttcctccccatttttattaaggtttctgtgttgaaccactaaatgctcaaagtactgttttccccctcttttttctactcaactaatct-aattcttatatacttttaaacgatcccagCGTGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                              ||| |  ||    ||  ||  || | |    | | |||| | ||   || |||| |  |||  |  ||| |   |  || |||||||| || ||||| || |||||||| ||||| || || |||||||| ||||| || || ||||| ||||||||||| |||||||||||||| ||||| |
------------------------------------------------------------gtaaact--cagttgttaccaagtg-tctcctccatgatctaattgtgatagccttcatgcttaatgactt-ctgttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                              ||| |  ||    || |||  || | |    | | |||| | ||   || | || |  | |  |  ||| |   |  || |||||||| || ||||| || |||||||| ||||| || || |||||||| || || ||||| ||||| |||||||||||||||||||||||||| ||||| |
------------------------------------------------------------gtaaact--cagttgttatcaagtg-tctcatccataatctaattgtgatagctttcatgcgtaatgactt-ctgctttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgc-caagca--ttttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                             |  ||| | | |  |  | |||  |   || |     |||| | | |  ||          |    ||   || |   || |  |||||||| || ||||| || ||||| || ||||| || || || ||||| ||||| || || ||||||||||| |||||||| || ||||||||||||||||
-------------------------------------------------------------gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctgattgctttcttttcc---tgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                         | |  |   || ||||    || ||   ||   | |||  | | |  |||| |     |   |  |  || |||    |    | |||||||| || ||||| || || ||||| || ||||| || |||||||| ||||| || |||||||||||||| ||||| ||||| ||||| || |||||||
-------------------------------------------------------gtaatgcatcctgtcaag---gtttagcccatacatgact--accattttgaaatgggtatttctgatactttcttttgtact-ctacagCGTGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttg---------cagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                              | ||||   ||| |    | ||  ||| || || | ||| |  ||   |   |  |  |||||  | || |||| || | |  ||    || ||||         |||||| |||||||||| |||||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || |||||||||||||| || || || |
----------------------------------------------ggtttc---aaattcatgactg--aagtatatttatatgttacttacatgtgtgctg-tgaat--atctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 8
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                                                      | | | |  |  | ||   ||  ||    | |       || | |         | |||||  |  ||||||| || || || || || || || || || ||||||||||| ||||||||||||||||| || || || ||||||||||| ||||| |
-------------------------------------------------------------------------------------gtatgtgaaattttattgtcgagctagagctgaactggcctttcct---------tacagCGCATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                                                      | | | |  |  | ||   ||  ||    | |    ||     || |       | |||||  |  ||||||| || || || || || ||||| || || ||||||||||| ||||||||||||||||| || || || ||||||||||| ||||| |
-------------------------------------------------------------------------------------gtatgtgaaattttattgtcgagctagagctgaac--tggccctttcc-------ttcagCGCATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGA

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|149070206|gb|EE158608.2|EE158608
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTTCCCTCGGTTCTGGGA
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGA
EST: gi|211532178|gb|FL123452.1|FL123452
EST:     G-CCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGG
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGG
EST: gi|211152796|gb|FL123506.1|FL123506
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGC
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGC
EST: gi|211529167|gb|FL123433.1|FL123433
EST:     GGCCTGNTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTTCG-TTCTTGGGAG-CACTT
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCT-CGGTTCT-GGGAGGCACTT
EST: gi|31355789|gb|CD440146.1|CD440146
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGACAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
EST: gi|148962822|gb|EE013742.2|EE013742
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACCCCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
EST: gi|148966031|gb|EE016965.2|EE016965
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGC
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGC
EST: gi|211154396|gb|FL123515.1|FL123515
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTC
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTC
EST: gi|149095258|gb|EE180885.2|EE180885
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCCTCG-TTCTGGGGAG-CACTTGTGCTA
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCC-TCGGTTCTGGG-AGGCACTTGTGCTA
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT
genomic: GGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                    tgcttac  putative branch site (score: 2)
              tgaattaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttgcagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA