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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG

Basic information

species Zea mays
transcript GRMZM2G389362_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 3
gctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG
| ||||||      |  |||||  ||  |||| | | ||| | | || | |||||||   | || || |  ||| ||| ||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||
gttagtac-----atacatgct--ataattttctattcatacaactggtaatctgaatttaacaccacccaccattttatatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCGACTCTTGTAATCAACAATAGACAATACAGAG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 3
gctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG
     |||| |||    |||||  ||  |||| | | ||| | | || | |||||||   | ||||| |  ||| ||| | ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||
---gttactacatac--atgct--ataattttctattcatacaactggtaatctgaatttagcatcacccaccattttatgtagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCGACTCTTGTAATCAACAATAGACAATACAGAG
















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|67022369|gb|CO451118.1|CO451118
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211315830|gb|FK969313.1|FK969313
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313814|gb|FK969304.1|FK969304
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313816|gb|FK969306.1|FK969306
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313815|gb|FK969305.1|FK969305
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313819|gb|FK969309.1|FK969309
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|32937726|gb|CF042545.1|CF042545
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313813|gb|FK969303.1|FK969303
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313817|gb|FK969307.1|FK969307
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|6445395|gb|AW179463.1|AW179463
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCA
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCA
EST: gi|67026759|gb|CO455508.1|CO455508
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|32937931|gb|CF042750.1|CF042750
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT

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), 48 (downstream exon)
Score: 170

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 97

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG
                tgttgat  putative branch site (score: 197)
                                         tccacttt  putative PPT
                                              tttgtata  TA-rich tract