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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacctcaattgtattgttgaggataggaaagggcagcatggtgggcggtggcggtgcggagtcgccttctgaatgatgtagaaactgaaagattctcgtaataattatttgagtacaatttctaatggacatattttccatgtgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 23
gtaagacctcaattgtattgttgaggat-aggaaagggcagcatggtgggcggtggcggtgcggagtcgccttctgaatgatgtagaaactgaaagattctcgtaataattatttgagtacaatttctaatggacatattttccat-gtgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT
||||||  ||| || | ||||||| | | ||  ||  |        |   |  ||   || |  ||     |  | | |    |    |||||  ||       | ||  | ||  |  |   ||||||| |||| | || |  || | | | ||||||||||||||||||||||  | |||||| ||||||| |||| ||||||||||||||||||||||||||| ||||||||||||
gtaagatttcacttttgttgttgatggtcagtgaacagttaataaatcttctatgcaagtacaaagaaatatgttcattagcatt---actgagtga-------agtagctgttgtatcagtctttctaaaggacttcttgttaattgagcttaacagGTTAAAGGTGTGAAACCATTACCTCTTCCTGAGATAGCTAGTCTTTTCATGAGCCTTCACTTGGCGGTTGCTCCTGGACTT
















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|211430870|gb|FL250418.1|FL250418
EST:     TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
EST: gi|37395386|gb|CF634973.1|CF634973
EST:     GCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
genomic: GCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
EST: gi|40336758|gb|CK370828.1|CK370828
EST:     TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
EST: gi|38502665|gb|CF972525.1|CF972525
EST:     TCTCCCAGGGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCCATGCCTCTTTCTGAGATGGCTAATCTTTTCAT
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCC-ATGCCTCTTTCTGAGATGGCTAATCTTTTCAT
EST: gi|67018440|gb|CO447189.1|CO447189
EST:     TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
EST: gi|166478248|gb|EG275286.1|EG275286
EST:     TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCT
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCT
EST: gi|211430871|gb|FL250419.1|FL250419
EST:     TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTG                         GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG
genomic: TCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 96

TGTATTGAATAAATTTTTGCAGACTATAACTCTTACCCCTGAAGAATTTTTCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

TGTATTGAATAAATTTTTGCAGACTATAACTCTTACCCCTGAAGAATTTTTCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT


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

TGTATTGAATAAATTTTTGCAGACTATAACTCTTACCCCTGAAGAATTTTTCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

TGTATTGAATAAATTTTTGCAGACTATAACTCTTACCCCTGAAGAATTTTTCTCCCAGTGGAAAGCGCTTACTGTTCATTCGCTGAAGGTTCAAGAAGTGgtaagacctc ... tgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaataattatttgagtacaatttctaatggacatattttccatgtgatgaacagGTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT
                      ttctaat  putative branch site (score: 68)
     aattatttga  TA-rich tract