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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtatttgtgtgagcatgaataggtcaccatgtgctcaatttcagtttgcttgaactttctgtcttttctcccatttggatatcagccctggcagct...

Basic information

species Zea mays
transcript GRMZM2G138349_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138349_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10480.3 (Oryza sativa), 5'ss of exon 4
CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtatttgtgtgagcatgaataggtcaccatgtgctcaatttcagtttgcttgaactttctgtcttttctcccatttggatatcagccctgg--cagct---
|||||||||| |||||||||||| | ||||| |  ||||||||||  || |||||||||||  | ||  |||| |||||||||||||||||||||   | | | ||| |     || || |||  |   || | || |  |    |       ||| |   |  ||  | |      ||   ||| |   
CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGCgtaagtattt---tcaacctgattcaa--actatctgcagagcatctgattcccagtggctgtaagactttgtagaacctgattgttcaatttgaatcagttggt

upper sequence: GRMZM2G138349_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 5'ss of exon 3
CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtatt--tgtgtgagcatgaataggtcac--catgtgctcaatttcagtttgcttgaactttctgtcttttctcccatttggatatcagccctggcagct
     |     |   | || || || ||||  || ||||| || | || ||||||||| ||||||||  | |||||||||||||||||||| |   ||  |||       ||| | |   | | ||||  |||   | || ||| ||     |  || |       |    |  | |    |       
---GTAAAAGAAGGTTAAAAGATTTATTGCTTAAAAGTGATAATCGCACTTGTGCTGATTGTGGTGCTCCAGATCCCAAATGGGCgtaagtttcactgcttgataccttttagtttatttcctttgctagattaatgatttcttcaaaccggtaactatatcatggtacacaattgaatgatatt----
















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|60672574|gb|DN475276.1|DN475276
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211169837|gb|FK962697.1|FK962697
EST:     ANTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTWAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211166491|gb|FK962680.1|FK962680
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211169840|gb|FK962700.1|FK962700
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168166|gb|FK962693.1|FK962693
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168168|gb|FK962695.1|FK962695
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168157|gb|FK962684.1|FK962684
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168159|gb|FK962686.1|FK962686
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|71768791|gb|DR966728.1|DR966728
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211169838|gb|FK962698.1|FK962698
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168160|gb|FK962687.1|FK962687
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168169|gb|FK962696.1|FK962696
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168161|gb|FK962688.1|FK962688
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168164|gb|FK962691.1|FK962691
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168167|gb|FK962694.1|FK962694
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168165|gb|FK962692.1|FK962692
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|31250107|gb|CD219131.1|CD219131
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCNAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168163|gb|FK962690.1|FK962690
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCTTCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|50334443|gb|CO529569.1|CO529569
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168162|gb|FK962689.1|FK962689
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCAT
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCAT
EST: gi|78087464|gb|DV515857.1|DV515857
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
EST: gi|211168156|gb|FK962683.1|FK962683
EST:     AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC                         ATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG
genomic: AGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAG

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: 47

CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGCgtaagtattt ... atctttgcagATCAGCTAATATTGGGGTATTCATTTGCGTAAAATGTTCTGGCGTCCATAGAAGTCTCGGTACACATATTTCAAAG