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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatccccttcgcacctcctcccgtgcatgtcggatactcggattcgttagatcttgacgggatgaatggatggatacctggcgttgagttgatttgtgcgcgtcgctgtgattgcag

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071071_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 1
AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgt------atccccttcgcacc---tcctcccgtgcatgtcggatactcggattcgttagatcttgacgg--gatgaatggatggatacc-tggcgttgagttgatttgtgcgcgtcgctg--tgattgcag------------------------------------
  || || |||||||| || ||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||||| ||||||| || |||||||      | | || |||| |    ||   ||| |     ||   | ||||    |||   | | | |||  |||   ||||||||  || | ||| |   | |  |||| ||  ||| ||  ||||| ||                                     
CCTTCCCGGAGAACGTCCCCCGCGTCATGCCGCCCACCCGCCTCCCCGCCGACTACTTCCCCGACCGCGTCCCAATCACCATCGTCGACACCTCCTCCAGgtccgctcacctccctcgcgctagatcgcgccgcggcccgcgatgaatcgggggtgttccct-tagtcggtagatttgtggatggactccgttgcgattt-tggccttgttcgtctcggtgattgattccatttctgtgtggttgattccatttctgtgtggatgcag

upper sequence: GRMZM2G071071_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 1
----------------------------------------------------------------------------AGTTTCCCGAG-AACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatccccttcgcacctcctcccgtgcatgtcggatactcggattcgttagatcttgacgggatgaatggatggatacctggcgttgagttgatttgtgcgcgtcgctgtgattgcag
                                                                             |   ||   |  |||| || |||||  ||||||||||||||||||||| ||| || ||| |||||||| |||||||||||||| ||||||| || |||||||    ||| | |  | ||||      | |   |||   ||| |   ||   | |||  |||  | ||   |||||       | |  |||||    |  |  | ||||  ||| |||
TGGCGGGCAAGCAGAGCTTGCGAGTCGTCGTCATCGGCGACCCTGGCACCGGCAAGTCCAGCCTCGTCGTGTCCGCCGCCACCGAGGCGACGTCCCCCGCgtactgccccccacccgcctccccgtcgactacttcgccgaccgcatccccatcaccatcgtcgacacctcctccaggt----cctccactgcccctc------acgctagatttgcgggtgtatttttttttgttggg--ggatttgtggatttt----gattcgttgacaattctgaattgctg--att-cag
















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|211367424|gb|FK987843.1|FK987843
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCG-T
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|148971580|gb|EE022295.2|EE022295
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|149010209|gb|EE042027.2|EE042027
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370078|gb|FK987855.1|FK987855
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370069|gb|FK987846.1|FK987846
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|31355399|gb|CD439756.1|CD439756
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|74244530|gb|DT652444.1|DT652444
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370076|gb|FK987853.1|FK987853
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCAY-ATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370077|gb|FK987854.1|FK987854
EST:     ATTATTTCCCCGACCGCGTCCCCATCACCATCTATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: ATTATTTCCCCGACCGCGTCCCCATCACCATC-ATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370071|gb|FK987848.1|FK987848
EST:     GATTACTTCCCCGACCGCGTCGCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|31353231|gb|CD437588.1|CD437588
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211367425|gb|FK987844.1|FK987844
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211367421|gb|FK987840.1|FK987840
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|148933977|gb|EC877975.2|EC877975
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370070|gb|FK987847.1|FK987847
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCG-T
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370074|gb|FK987851.1|FK987851
EST:     GATTACTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211367423|gb|FK987842.1|FK987842
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCAYNATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAKTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT
EST: gi|211370073|gb|FK987850.1|FK987850
EST:     GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCNGT
genomic: GATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGT

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), 39 (downstream exon)
Score: 87

AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 64

AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 33

AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

AGTTTCCCGAGAACGTGCCTCGCGTCATGCCCCCCACCCGCCTCCCCGCCGATTATTTCCCCGACCGCGTCCCCATCACCATCATCGACACGTCGTCCAGgtatcccctt ... gtgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGTCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGT