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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatgtactgtagtatcctgctgcaattgattcacttgatttcccttaatagctgaaacacctcatttaaaaaaaaatcattgcagtgctctgctcatctagaacctgaacatgcttaggactaagaggctttgttgttgttgtattgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 7
gtgagcatgtactgtagtatcctgctgcaattgattcacttgatttcccttaatagctgaaacacctcatttaaaaaaaaatcattgcagtgctctgctcatctagaacctgaacatgcttaggactaagaggctttgttgttgttgtattgtt-gcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT
                                                         ||| |      ||||||   | |    |||  ||||| |  ||   |  |   ||  |   |     |   |||  ||   ||    ||   ||||   ||||||||||||||| |||||||| ||||| ||||| |||| | | ||||||||| |||||||||||||||||||||||||||| |||||  | |||||||||
--------------------------------------------------------gtgaga------atttaattgacatcttttgttgtgctttattccattc-attttgctccaacaagtaaagcagactctccctttccttttatttgtccacagTGCTCATCTTGAGTGGAATCTCGATGGTCTTCTAGAGATGATCTGGGAATACCTGGATTTGGTTAGGATATACACAAAACCGAAAGGTTTAAACCCAGAT

upper sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgagcatgtactgtagtatcctgctgcaattgattcacttgatttcccttaatagctgaaacacctcatttaaaaaaaaatcattgcagtgctctgctcatctagaacctgaacatgcttaggactaagaggctttgttgttgttgtattgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT
                                                                    |  |      |||| |  |    | | |||  ||    ||| ||   |   ||   | |||||       || ||    |||  ||||||||| ||||| || ||||||||||||||||||||||| ||| ||||||||||||||||| |   | | || ||||||||||| || |   |||| || |||
------------------------------------------------------------------gtaaatgttgttaaattaccggcaggatttgcg-at---aaacttgtttacttttgccattaagatataaatttatt----tatc-ttgcagTGCGCATCTGGAGTGGAATCTTGATGGACTTCTGGACAAGATATGGGAATACTTGGATCTAACTCGAATCTACACAAAACCAAAGGCAATGAATCCGGAT
















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|60398886|gb|DN231702.1|DN231702
EST:     GAGCTGG-AATCTTNGGA-AAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: GAGCTGGAAATCTT-GGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|60358587|gb|DN225560.1|DN225560
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|74240037|gb|DT647951.1|DT647951
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|14203739|gb|BG837416.1|BG837416
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|211345618|gb|FL479628.1|FL479628
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|211493768|gb|FL172984.1|FL172984
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|71758265|gb|DR956202.1|DR956202
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|32933065|gb|CF037877.1|CF037877
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|211493769|gb|FL172985.1|FL172985
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|30088250|gb|CB886455.1|CB886455
EST:     CCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
EST: gi|22542064|gb|BU092502.1|BU092502
EST:     CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAG                         TGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA
genomic: CTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATA

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: 253

GGATTTACACTCCTTGCGTATATGTTGTCAACAAGATTGATCAGATAACACTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 247

GGATTTACACTCCTTGCGTATATGTTGTCAACAAGATTGATCAGATAACACTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GGATTTACACTCCTTGCGTATATGTTGTCAACAAGATTGATCAGATAACACTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 224

GGATTTACACTCCTTGCGTATATGTTGTCAACAAGATTGATCAGATAACACTCGAGGAGCTGGAAATCTTGGACAAACTTCCCCATTACTGCCCGGTTAGgtgagcatgt ... attgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaacctgaacatgcttaggactaagaggctttgttgttgttgtattgttgcagTGCTCATCTTGAATGGAATCTTGATGGACTTCTGGAGAAGGTATGGGAATACTTGGATTTGGTTAGGATATACACAAAACCTAAAGGGCTGAACCCAGAT
                                         ttgtatt  TA-rich tract