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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagcataatcatttgcttcgtgtcttagtgtgccacatgcgtaccatggttgtttcttgaatgtaagttttctcatggaagtctgttaacattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG

Basic information

species Zea mays
transcript GRMZM2G007489_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 5
gtaagtagcataatcatttgcttcgtgtcttagtgtgccacatgcgtaccatggttgtttcttgaatgtaagttttctcatggaagtctgttaacattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG
       | |      ||    | |  | |||  ||    ||| | |      | || ||||      |||  |||||||||   |    ||         ||||| | ||||    |||||||||||||||||||||| ||||| || || ||||| || |||||||| ||||||
-------gtaagtcagttaatattgcttgttaccgt----cattcattttgctggtggttctcatgcataaaatttctcatgagggatcctttgttcatgtcagCCGAAGTGG---AGTGACCTTGATGTCAACCAGCATGTGAACAATGTGAAGTATATTGGTTGGATACTTGAG

upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ13354 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtagcataatcatttgcttcgtgtcttagtgtgccacatgcgtaccatggttgtttcttgaatgtaag-ttttctcatggaagtctgttaacattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG
                                  |||    || | |  ||   |  |||||      |  | |||| | |  | |   | ||  ||||   ||||| |||      || ||| | ||  | |||||||||||||| ||||| ||||||||||| ||||| || |||
----------------------------------gtga-gtatccatctcactttcctttctctttcctgcgctttttttaaagtatcatctttgcatttg-cagCCAAGGCA---TGGAGACTTGGACATGAACCAGCACGTGAACAACGTAAAGTACATCGGATGGATGCTCGAG
















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|21480804|gb|BQ577487.1|BQ577487
EST:     GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACT                         CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
genomic: GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
EST: gi|87154342|gb|DY399131.1|DY399131
EST:     GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACT                         CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
genomic: GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
EST: gi|26455441|gb|CA827024.1|CA827024
EST:     GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACT                         CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
genomic: GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
EST: gi|6021504|gb|AW066432.1|AW066432
EST:     GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACT                         CCTAGGTGGTGGGGCGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
genomic: GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
EST: gi|21390363|gb|BQ528412.1|BQ528412
EST:     GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACT                         CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG
genomic: GCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAG

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: 151

CCGCGCAGCCATAACAGATGAGCAGAGCGAGAAACTGGCTAAGCCAGGGAGCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 41

CCGCGCAGCCATAACAGATGAGCAGAGCGAGAAACTGGCTAAGCCAGGGAGCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 38

CCGCGCAGCCATAACAGATGAGCAGAGCGAGAAACTGGCTAAGCCAGGGAGCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CCGCGCAGCCATAACAGATGAGCAGAGCGAGAAACTGGCTAAGCCAGGGAGCACTGCTGGTGGCGATGCTATGAAGCAGTTCATGAGAAAGGGGCTCACTgtaagtagca ... cattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggttgtttcttgaatgtaagttttctcatggaagtctgttaacattgaacagCCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG
                                       tgttaac  putative branch site (score: 71)
                   taagtttt  TA-rich tract