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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatcattctttgttcttttttacaccgtcctcatttatgaccttactaaaaaatcgtatttatccttctacag

Basic information

species Zea mays
transcript GRMZM2G466281_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g02750.1 (Oryza sativa), 5'ss of exon 14
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatcattctttg-ttcttttttacaccgtcctcatttatgaccttactaaaaaatcgtatttatccttctacag-------------------------
                                     || |||||||||||||||||||| |||||||| ||||| ||| |||| |||||||||||||||||  |||| |   || | |  |  ||||||| || | |||| ||||  | |   | |  |   ||  |  | | || || |||  |  ||                            
-------------------------------------GGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATGgttgttgcct---aatcacctttgttctttggttttgttttccaccaccttttataagtaatatatgatgata-cgcatatattttgttatgattaaacattgtgcctccctttgcag

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G14210.1 (Glycine max), 5'ss of exon 15
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatcattcttt----gttcttttttacaccgtcctcattta-----tgacctt-actaaaaaatcgtatttatccttctacag
                                     ||||| |||||| |||| ||||| ||||||||||| |||||| ||||||| |||||||||||||||   |||  |  |    |||  | ||||     ||  |||||  |    | | ||||      || || | | || ||||   |    |  |    |   
-------------------------------------GGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATGgtataagctatgtcacttgaatgttactttctgaattactttttttagatgcttgatttggctgctgtccctcattataaaactttgaaaacacaatgat--

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G08720.1 (Glycine max), 5'ss of exon 15
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaat----cattctttgttcttttttacaccgtcctcattta-tgaccttactaaaaaatcgtatttatccttctacag---
                                     || || |||||| |||| ||||| ||||||||||| |||||| ||||||| |||||||||||||||   |||  |  |    |||    ||||||   ||  |||||  |    | | ||||  |     | |   |  ||   |  |||      |||    
-------------------------------------GGGAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATGgtataagctgtgttacttgaattttacattctgaattacttttttgagatgcttgatttggttgttgtccctcattataaaacctatgaaaacacaatga

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: AT3G25585.4 (Arabidopsis thaliana), 5'ss of exon 13
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatca--ttctttgttcttttttacaccgtcctcatttatgaccttactaaaaaatcgtatttatccttctacag
                                     |||||||||||||| |||||||| ||||| ||||| || || |||||||||   ||||| ||||||         |||| ||||| |  |||||  | ||   | | |  ||  || |   || ||| |||||         ||    |||  ||||
-------------------------------------GGAAGAATGATTCTAGCTCACTTATGTGACGAACCAAAAGGATTGAAAACAAACATGTGTATGgta---------aaagtccaataactttcttcttgctcgatcaaaatgttttcttcgttgtcctcactaa-------ctttctctcttgcacag

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 5'ss of exon 14
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatcattctttgttcttttttacaccgtcctcattt--atgaccttac--taaaaaatcgtatttatccttctacag
                                     |||||||||||||| ||||||||||||||||| || || ||  | ||||||   ||||||||||||  | |    ||       |      ||  ||  | ||||    | ||  |||  |  |  | ||  |   ||||| | ||  ||    | |||
-------------------------------------GGAAGAATGATTCTTGCTCACTTGTGTGATGAGCCTAAAGGACTAAAAACAAACATGTGCATGgtaaat-ccgataattttttcttgccaatttctccgtcttactggatactggttttgaaaatgtaaccttgtgaaatctttttactcaaaatgcag

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 15
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgcttggaaagcccaatcattcttt-gttcttttttac-accgtcctcatttatgaccttactaaaaaatcgtatttatccttctacag------
                                     ||||| ||||||||||| ||||||||||||||||||||||| |||||||| || ||||||||||||  |  |     | ||  |  ||| ||  ||| | |   ||    |||    | | |  || | |        |  |      |  |  |        
-------------------------------------GGAAGGATGATTCTGGCACACTTGTGTGATGAACCCAAGGGCTTGAAAACTGGAATGTGCATGgtatgttgtattctaaccagacaattattgagttatctgccactgtggtctctctcttttcccctccctctggcccccacacgcgccccccccctttccc

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 5'ss of exon 14
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtactt----gcttggaaagcccaatcattctttgttcttttttacaccgtcctcat-ttatgacctt-actaaaaaatcgtatttatccttctacag-----
                                     ||  |  | ||||| |||||||||||||||||||||||||||||||| || || ||||||| ||||| |    | |   ||| |  ||||   | | || |    | ||    |  ||||  | |    || ||||  | ||  |   ||   | | | ||     
-------------------------------------GGTCGGCTAATTCTTGCTCACTTGTGTGATGAACCCAAGGGTTTGAAGACTGGAATGTGCACGgtacgtcgccgttcttaaacctaaatcg--catagtccaacatcacgtatttgtcatgctgtcttgttcactaggagatactggctaatat-caagagaaagc

upper sequence: GRMZM2G466281_T03 (Zea mays), 5'ss of exon 1
lower sequence: PP1S269_30V6.2 (Physcomitrella patens), 5'ss of exon 14
TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtactt----gcttggaaagcccaatcattctttgttcttttttacaccgtcctcatttatgaccttactaaaaaatcgtatttatccttctacag------
                                     ||  || | ||||| || ||  | |||||||||||||| |||||||| ||||| ||||||| ||||  |    | ||  ||| |  ||| |     ||       | |  ||  |   | ||  |  ||  ||||    |  ||  | |  |   |         
-------------------------------------GGCCGACTAATTCTTGCACATCTATGTGATGAACCCAAAGGTTTGAAGACAGGAATGTGCACGgtaagttgcagtttctaaacctgaattacctagtgcaaggcgtcattccagctgtagttcagttct--ctaatgggtgttagctgttttaaaatgattactt

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|71309475|gb|DR791024.1|DR791024
EST:     TGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATG                         TCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTT
genomic: TGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgctt ... ccttctacagTCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTT




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 125

TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgctt ... ccttctacagTCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTTGATGATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgctt ... ccttctacagTCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTTGATGATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgctt ... ccttctacagTCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTTGATGATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

TGAACATTACTTTACATCTGCTTATATTGCTCCACAGGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATGgtacttgctt ... ccttctacagTCCCTTGCGTATTTTCCATTTGCAATTGCAAACGCGTTGACTGCCCGGCTTGATGATGG