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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattgtcaaattgaagtcttttacttcactatccttgataagtttactgaaagttgtttctgatgagctggaagcctggaagttgaaaattgggg...

Basic information

species Zea mays
transcript GRMZM5G885392_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 5
ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattgtcaaattgaag-tcttttact--tcactatccttg--ataa-gtttactgaaagttgtttctgatgagctggaagcctggaagttgaaaattgggg
|||||||||  |||||||||| || || ||||| |||||||||||||||||||| |||  |  |||||| ||| |  | |||   |    |||| |    ||  | | ||||| |  ||   | || |  |||   | |      |   ||       
ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattcaagataatataccaattgagatccatacagtactgctcactgacatgtgggcccgagggtctgtggggccctctctcataat------

upper sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ34397 (Selaginella moellendorffii), 5'ss of exon 6
ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattgtcaaattgaagtcttttacttcactatccttgataagtttactgaaagttgtttctgatgagctggaagcctggaagttgaaaattgggg
  | |||||||| ||||| || ||||||||||| || ||||||||||||||||| |   |||      | || ||| |||||||            |   |  ||     | |                                       
TGTGTTCTTTTTAGATGACTTAACGGGATTTGAGATAACATATCTTCTTGAGgtgaa-gttgatgctgttaattctcttacttcctctcatccatcacactctctttgtatag---------------------------------------

upper sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ23658 (Selaginella moellendorffii), 5'ss of exon 7
ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattgtcaaattgaagtcttttacttcactatccttgataagtttactgaaagttgtttctgatgagctggaagcctggaagttgaaaattgggg
  | |||||||| ||||| || ||||||||||| || ||||||||||||||||| |   |||      | || ||| |||||||        |   | | |  ||     | |                                       
TGTGTTCTTTTTAGATGACTTAACGGGATTTGAGATAACATATCTTCTTGAGgtgaa-gttgatgctgttaattctcttacttcctctcatctatcacgctctctttgtatag---------------------------------------

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|18178811|gb|BM380021.1|BM380021
EST:     TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|88748429|gb|DY532570.1|DY532570
EST:     GGATGATTTCACGGGATTTGAAATCACATATTTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCCCTGCCTTTA
genomic: GGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|32924858|gb|CF029670.1|CF029670
EST:     TCTTCTTCTTGGATGATTTCACGAGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATATTCACATGGTTCGCCGCACTGCCCTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|71760700|gb|DR958637.1|DR958637
EST:     TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|32925008|gb|CF029820.1|CF029820
EST:     TCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATATTCACATGGTTCGCCGCACTGCCCTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|32926006|gb|CF030818.1|CF030818
EST:     TCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATATTCACATGGTTCGCCGCACTGCCCTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|86468794|gb|DY235164.1|DY235164
EST:     GGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: GGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|6827379|gb|AW331022.1|AW331022
EST:     TCTTCTTTTTGGATGATTTCACGGNATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGCTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|32926318|gb|CF031130.1|CF031130
EST:     TCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATATTCACATGGTTCGCCGCACTGCCCTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|78074964|gb|DV503398.1|DV503398
EST:     TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|13381842|gb|BG458517.1|BG458517
EST:     TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|148942558|gb|EC887577.2|EC887577
EST:     TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATTTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|32942294|gb|CF047113.1|CF047113
EST:     TCTTCTTCTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATATTCACATGGTTCGCCGCACTGCCCTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|211475315|gb|FL222267.1|FL222267
EST:     CTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: CTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|110538710|gb|EE042664.1|EE042664
EST:     TTTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATTTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: TCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
EST: gi|211475316|gb|FL222268.1|FL222268
EST:     GATGATTTCACGGGATTTGAAATCACATATCTTCTTGAG                         TTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA
genomic: GATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTA

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: 39 (upstream exon), 20 (downstream exon)
Score: 3

ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCC


Block sizes: 38 (upstream exon), 12 (downstream exon)
Score: 1

ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 62

ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattg ... attcacgcagTTGCCGGAGCCTTTCAGTTTCATCTTCACATGGTTCGCCGCACTGCCTTTAATATTTTGGGTAGCGCAGGCGATCACTAATGTCATAGTGAAGGACTTCC