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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattattactttccaagagtatttgttgttttcacttctagaagcatttgtagggatgattattaacttgaggttaggacatccatgtattttccttt...

Basic information

species Zea mays
transcript GRMZM2G094255_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 5'ss of exon 3
GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattattactttccaagagtatttgttgttttcacttctagaagcatttgtagggatgattattaacttgaggttaggacatccatg----tattttccttt---
|||||| ||||| |||||||| || |  ||||| ||||  || ||||| || || ||||| ||||||||||| || ||||| |||||||||||||||||||| ||| || |||||         || |  |||   |||||||||  | ||||||| || ||||| || |  ||||||||  ||||||      ||  | ||||   
GGCATCTCATGGGCTCTTTGACGTATGTGTTAAGGCAAAGGGTGACACTCACATCGATGACCATCACTCAAACGAAGACATCGCTTTGGCAATTGGAACGgtaattgttgctttcac------cttatcatttctgcttctagaaatacttgtagg-atcattatgaattgaaggttagggtatccataatttcatacttcttttcc
















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|76010862|gb|DT938032.1|DT938032
EST:     CAAATGAGGACATTGCTTTGGCATTTGAAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: CAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|31355338|gb|CD439695.1|CD439695
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006666|gb|FL081503.1|FL081503
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|71327961|gb|DR800622.1|DR800622
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTCTGGCAATTGAAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006664|gb|FL081501.1|FL081501
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006671|gb|FL081508.1|FL081508
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|50325237|gb|CO520363.1|CO520363
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006662|gb|FL081499.1|FL081499
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006669|gb|FL081506.1|FL081506
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|88757021|gb|DY541162.1|DY541162
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|91056439|gb|EB166857.1|EB166857
EST:     ATATTGATGATCATCACTCAAATGAGGACTTTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTGGGTGATCGAAAGGGAAT-AACCG
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCG
EST: gi|31611949|gb|CD568571.1|CD568571
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211003886|gb|FL081493.1|FL081493
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|149110134|gb|EE293952.2|EE293952
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|101397352|gb|EB820599.1|EB820599
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|211006657|gb|FL081494.1|FL081494
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACG                         GCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT
genomic: ATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCAT

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), 49 (downstream exon)
Score: 36

GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 51

GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 38

GGCATCACATGGACTCTTTGATGTCTACGTTAAAGCAATAGGCGACACCCATATTGATGATCATCACTCAAATGAGGACATTGCTTTGGCAATTGGAACGgtgattatta ... gtctatgtagGCACTACTTGAAGCACTTGGTGATCGAAAGGGAATTAACCGATTTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG