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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcttcggacccatccatccctgcgtttctgtggacattctgttctgttctgcgttcccccatctcaatctgacttggttatctgtgggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT

Basic information

species Zea mays
transcript GRMZM2G052546_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 2
gtgaggc--------ttcggacccatccatccctgcgtttctgtggacattctgttctgttctgcgttcccccatctcaatctgacttggttatctgtgggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
||||  |        |||    |||| ||   |   |||| |      ||| |     | || ||  ||||  || |    ||   || | | ||  ||   |  ||| ||||||| || ||||| ||||||||||||||||| |||||||| 
gtgacccctcttccattccattccattcacgtccttgttttttcccctattattgatggatcggc--tcccttatttgttcctctttttgatgtccatga-tgactagACGATGGTTCGTGGCGGGAGTCGCCGATCAAACACTGTCAAAACC
















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|148952817|gb|EC898809.2|EC898809
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|15427195|gb|BI543017.1|BI543017
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|211183157|gb|FL428740.1|FL428740
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|91052216|gb|EB162634.1|EB162634
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|211478786|gb|FL377818.1|FL377818
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|76914764|gb|DV165677.1|DV165677
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|149081546|gb|EE170685.2|EE170685
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|211346141|gb|FL398010.1|FL398010
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|211266638|gb|FL405762.1|FL405762
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
EST: gi|91876121|gb|EB406078.1|EB406078
EST:     CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTG                         GCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
genomic: CTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT

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: 45 (upstream exon), 11 (downstream exon)
Score: 4

GGAGCCTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 17

GGAGCCTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 15

GGAGCCTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT


Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 11

GGAGCCTCCAATCGTGGGGTCCAGGTCGATGAGGCGGCCCTCTCCGCTGAATCTGgtgaggcttc ... gggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgttctgcgttcccccatctcaatctgacttggttatctgtgggcggttagGCGATGGTCCGCGGCGGCAGTCGCCGATCAAACACCGTCAAAACT
                          atctgac  putative branch site (score: 11)