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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcactccttatgttctatgactttgtgttgtcagtctatattactgacatcactcttttctttttcag

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 9
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcactccttatgt-tctatgactttgtgttgtca--gtctatattactgacatcactct-tttctttttcag
|||  |||||||||| || ||  |||||||||||||||| |||||||||||||||||||| |||||||| ||||| || |||||||||||||||||||||||||| || || | ||    || ||| ||||||||||||   | |  ||||||||  ||| ||| |||||||   ||
CACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaatcttcattcacctgtga-tttgtgttgtcacgatttgcattactgatttcattctgtttctttcctag

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 9
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgt--ttggcactccttatg--ttctatgactttgtg--ttg----tcagtctatattactgacatcactcttt--tctttttcag----------------------------------------------------------------
|||  |||| ||    ||  |  | || ||  | || ||  ||  ||||||||||||||| || ||||| || ||||| || ||||||||||| || |||||   |  ||||    |    ||  |  | ||| |   |||    ||  | |||     ||  || |   |||  |  | ||||                                                                 
CACTGACTATATCGTAGACGTTGTTTGTAAAAGAGCTGAAATTAATTACAACTATGGTGTCATTCTTATCCCTGAAGGTCTAATTGATTTCATACCTGAGgtatctatcactttgcacagttttcacaatttttttacttgcatttccctttatgcacttggaattatattttagtgctgttcatgtacaaccagtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 9
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcactccttatgttctatgactttgtgttgtcagtctatattactgacatcactctt----ttctttttcag--------------------------------------------------------------------------
|||| |||| ||    ||| |  | || ||  | || ||  ||  |||||| ||||||||||| ||||| || ||||| || ||||||||||| || ||||| |    | | ||    | |      || | || | |  || | || |   |    | |||    || | ||| ||                                                                          
CACAGACTATATCGTAGATGTTGTTTGTAAAAGAGCTGAAATTAATTACAATTATGGTGTTATTCTTATCCCCGAAGGTCTAATTGATTTCATACCTGAGgtatctatcactttgcagttttcacaattattttttta-cctgtgtttccccctctgcacttgggattatgttttagtgttgttcatgtacaacctgtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcac--tccttatgttctatgactttgtgttgtcagtctatattactgacatcactcttttctttttcag--------------------------
|||| |||||||    ||| | |||||||| ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || || ||||| ||      |  | |     ||  |  |  |  | | |  |   |||| |   ||   |||| |    |   |                          
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccg-attaatataattgttcttcttaactgatgattaattttatttcatgacttctcag

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 9
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcactccttat--gttctatgactttgtgttgtcagtctatattactg-acatcactcttttctttttcag------------------------
 ||| ||||||||  |||| |  ||||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||| || ||||| |   | |  ||||  |   |||   |||      |   | | |  |  ||   ||   | |  | ||   ||                         
TACAGACTACATTGTTGATGTTGTCTGCAAACGTGCAGAACTTGGTTACAACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatattgattataagacttatttatttaacccttttttttgtcctcttgtgaatgggtatccttttaagcaaacttgtcttgctttttttcaagtt

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|67015202|gb|CO443951.1|CO443951
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCAGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|67014279|gb|CO443028.1|CO443028
EST:     GCCTGATTGATTTCATCCCAGA-                         GTTCAAAAACTCATCGCAGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: GCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|31348678|gb|CD433035.1|CD433035
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|211507301|gb|FK969868.1|FK969868
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGATATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|6021533|gb|AW066461.1|AW066461
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|32831581|gb|CD971259.1|CD971259
EST:     ATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCAGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|31353849|gb|CD438206.1|CD438206
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
EST: gi|6587580|gb|AW244898.1|AW244898
EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTT

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: 471

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGCCTGAATCAAGGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 499

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGCCTGAATCAAGGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 475

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGCCTGAATCAAGGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcact ... tctttttcagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTGGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGCCTGAATCAAGGGAGC