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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa...

Basic information

species Zea mays
transcript GRMZM2G114126_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactat---gttccgaattagacttcttgagatt-------tacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
||||||||||||||||||||||||  |||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||||||||| |     ||  | |||||   |   ||  |       |   ||   | | | ||   | || ||||   | |  |  |||| |    || || |       
GAAGATGATGCACAAGTACATAGGGGCAGATGTTACATCACTTGTGACACTTCCGGTCATCATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCAGAGgtttgtactgttaaactcacatttagagcgcagtagcctgtgttcgtcttctcatcctgtgcattggcagaatgt---tacgttcatttgcttagcgtagtat-------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G39880.1 (Glycine max), 5'ss of exon 3
-GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatt--tacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa--------
 ||| |||||||| |||||  | || || ||| | |||||| | ||||||||||| || || |||||||||||||||||||| |||||||||||||||||||| |||  ||| | |     |  | || ||     |  |||| |  | |   || | | |   |  | ||||  |  ||   |||    | ||| | | | |        
GGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCGGTTATCATTTTTGAGCCAATGACAATACTTCAGAAAATGGCTGAggtctgttttatatactttgctgcatttgtttttgctattacattaac-acaaactatttagcaaattctctgtca--gtacaatctcattggtcataatacattttcaca

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G15930.3 (Glycine max), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagactt-cttgagat-ttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa---------
||| |||||||| |||||  | || || ||| | |||||| | |||||||||||||| || |||||||| |||||||||||||||||||||||||||||||| ||| |||| | |     |  | || |||  | | ||||| |  | |   || | | |   |  | ||||| |  ||   |||    | ||    | | |         
GAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCAGTTATCATTTTTGAACCAATGACAATGCTTCAGAAAATGGCTGAGgtctgtgctatatactttgctgcatttgcttttgctattacattaac-acaaactatttagcaaattttctgcca--gtacaatctcattggttgcaatatattttcacag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G04210.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa--
||||||||||||||| || || || |||||||| |||||| | || ||||| ||||| || |||||||| |||||||| ||||||||||||||||| |||||||| ||   | ||    |||   ||  ||   | | |  ||   |  | |       |  ||| |  ||| ||| |||| | |||   | ||  ||    
GAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGCTTCAGAAAATGGCAGAGgtttgcaca--gctctattttattttttgtgttttctgctttgttaaattgctttatttgtttgtattggcacttgattgagctttgaattgttcgaactag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggat-gtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||| ||||| || || || ||||| |||||| | |||||||| ||||| || || ||||| |||||||| ||| |||||||||| |||||||  | | |||  ||     || | | |  |      ||| |||    | ||      |  ||| |  | || ||||| ||||                   
GAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACACTACCAGTTATTATATTTGAACCAATGACTATGATTCAGAAAATTGCTGAGg--tatgctaacttttagttttgccattgttgatgatac-ctgaatttgtagtgtcaattgattgaatttgaaattgcttgaaatag--------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||| ||||| || || || ||||| |||||| | |||||| | || || || || ||||| |||||||| ||| |||||||||| ||||||||  |   ||   |  |  ||    || ||||   | ||  |   |        |    |  ||  | || || |      | ||||   |         
GAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGATTCAGAAAATTGCTGAGgtcggc-ttactcttagttttgccattgttgatgat-accttaatctgtagtgtcaattgattgaatttgaaaattgaaattgcttgaaatag-------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||| ||||| ||||| || |||||||||||  | || || ||||| || || |||||||| || ||||||||| | |||||||||||||||||||||    | ||     ||||| |   ||| |  |    | ||         ||   | |  ||| |    ||  |  ||  |||| |||| |  |  
GAAGATGATGCAGAAGTATATAGGGTCTGATGTTACATCTATGGTTACTCTTCCTGTGATCATTTTTGAACCCATGACAATGTTGCAGAAAATGGCTGAGgtttgtg--gtcttagattttagattatatgaaagatcttttagcttctggtttctattgaacatgttt-tggtttctccat--ttgttgtctctgcag-

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa-
|||||||||||| || || ||||| || ||| |||| ||| | ||||| ||||| ||  | || |||||||| ||||| ||||| ||||| |||||||||||| ||  |||    | ||||     || || | ||     |    || |     |      ||||| | |  |  | | |   |||     ||   | | 
GAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGCTCCAGAAGATGGCTGAGgttagtgttatacatctaatt----ctcctgtgtttg----taagtatttgttgttttt---tgtgtgtactgtattataacatttgcaaatttctcacag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtact-atgttccgaatta--gacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||| |||||||||||||| |||||||||||| | ||||| ||||| || || |||||||| |||||||||||||||||||||||||| ||||||||| || ||| ||  |  |   || || ||    | |    | |   | |  ||    | ||||      ||||  | ||  |  |||      ||    
GAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGCTTCAGAAAATGGCGGAGgtttgtgctcatgatcacatctgatgatttgttcctgtctgatatagt--tttgtaatccgatgatgc-----caatgatatgtgctctgtttctggtag---

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgt--tccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||| ||||| ||||| |||||||| || ||| | ||||||||||||||  | ||||||||||||||||||||||||||||||||||| || || ||| | || |  |  | || ||     ||||  ||||   |||     |    ||  ||  ||| ||     |||    ||  |    |  | | | | 
GAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCAGAAgtatgtgccatctagtttgtataag----tttgatgtttatcttggtagattgtctct--agcctgtttcaaatgttgca-aattgtgaatgcttgtgacag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtactatgttccgaattagacttcttgagatttacact--ggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa
|||||||||||||||||| ||||| || ||||| |||||| | ||||||||||| || || |||||||||||  |||| || || |||| |||||| ||||||| |   || ||     ||| |||   |   | | |   |  |||     |   | |         |      ||  |   |   ||    || | | | 
GAAGATGATGCACAAGTATATAGGCTCTGATGTCACATCAATGGTGACACTTCCTGTTATGATTTTTGAGCCGTTGACTATACTGCAGAGAATGGCAGAGgttttt-tcatttttgtgtttaaactgtattgcagtaatgttagggctgctcaaggcagttcagctgattgaatgttactaactgtatgatacctgttacag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 3
GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgt-ttgtactatgttccgaattagacttcttgagatttacactggccatctacaactgaaggatgtgtctgcaattgtttgatccttgtcgtctttaaaaa-
||| |||||||||||||||||||| || ||  |||| ||| | ||||||||||||||||| || |||||||| ||||| | ||||||||| ||||||||||| || |  ||  ||     |  |    |   | || |         ||||   | |  |  |||  ||||| ||    ||||  |||     | |  | | 
GAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGCTTCAGAAGATGGCTGAGgtatttttttactttttttgtgcgtggccgcaaaatatttggctttaatctttgagtacaaaatgattctgctatc-cgtgatg-ttgcaaattctgtatac

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|211354689|gb|FL118768.1|FL118768
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|211354687|gb|FL118766.1|FL118766
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAG
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAG
EST: gi|211354688|gb|FL118767.1|FL118767
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC-A
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|91055718|gb|EB166136.1|EB166136
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|67040089|gb|CO466344.1|CO466344
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|74236529|gb|DT644443.1|DT644443
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|26558339|gb|CA830574.1|CA830574
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|211354691|gb|FL118770.1|FL118770
EST:     TTCCAGTCATATTTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACCTGTGAGTTGTTAGAC
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATAC-TGTGAGTTGTTAGAC
EST: gi|211354686|gb|FL118765.1|FL118765
EST:     TTCCAGTCCTAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|149105113|gb|EE290596.2|EE290596
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|148961873|gb|EE012659.2|EE012659
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|78120437|gb|DV538821.1|DV538821
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
EST: gi|32801394|gb|CD953630.1|CD953630
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATC
EST: gi|87155561|gb|DY400350.1|DY400350
EST:     TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAG                         TTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA
genomic: TTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 105

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 215

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

GAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGCTTCAGAAAATGGCTGAGgtttgtacta ... ctgaatgcagTTGATGGAATACTGTGAGTTGTTAGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT