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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgaccttgtctgcccgtccgatggctctcacagtctctctcctccctcgagaaccccccccccccccccccccccccccttccgatttcgatttgaccttgtgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG

Basic information

species Zea mays
transcript GRMZM5G885700_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G885700_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g34680.1 (Oryza sativa), 3'ss of exon 1
gtgagttgaccttgtctgcccg---tccgatggctctcacagtctctctcctccctcgagaaccccccccccccccccccccccccccttccgatttcgatttgaccttgtgt---tcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG
||  |||   |||  || | ||   ||| ||  ||    |             | ||  |           |     |    |    ||  ||    ||    |  ||| |     |  | |||||  |||| || |||||||||||||| ||||| |||| ||| ||||| ||||||||||
gtccgttcctctttcctcctcgaattccaatcccttcttctaatgggagagagcttcttgttggtttgattcggattcggatctgatctctcgtccgcgccacgcgcttatacatgttgttagGGTTCCGCAGGATCTGGTCGTCGCCGGTGGCCCATGCGCGCTCTACAAATGGGTGCGAG
















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|50329241|gb|CO524367.1|CO524367
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|89762364|gb|DY689981.1|DY689981
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|211050924|gb|FL038266.1|FL038266
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|71444956|gb|DR826006.1|DR826006
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|149088134|gb|EE177283.2|EE177283
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|211050923|gb|FL038265.1|FL038265
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGA--SCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|211484014|gb|FL012872.1|FL012872
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
EST: gi|148935905|gb|EC879955.2|EC879955
EST:     CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGAGAAGGAGTG                         GGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG
genomic: CGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTG

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: 40 (upstream exon), 47 (downstream exon)
Score: 25

AGCCCTGCCCCTCTCCTCCAGCGCCGCTCGCCAGCTCTCTGCCCCCGCCGCGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG


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

AGCCCTGCCCCTCTCCTCCAGCGCCGCTCGCCAGCTCTCTGCCCCCGCCGCGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 38

AGCCCTGCCCCTCTCCTCCAGCGCCGCTCGCCAGCTCTCTGCCCCCGCCGCGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 18

AGCCCTGCCCCTCTCCTCCAGCGCCGCTCGCCAGCTCTCTGCCCCCGCCGCGCCCAGAGATGCAGATCCCCCACCGCCGTTACCGCTGGGTGAAGGAGTGgtgagttgac ... tgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccccccccccccccccccccccttccgatttcgatttgaccttgtgttcttcagGGTCTCGCAAGAACTGGTCGTCGCCGGAGGCCCCTGCGTGCTGTACAAGTGGGTGCGAG
                                  atttgac  putative branch site (score: 18)
                                             tgttcttc  putative PPT