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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggcaggttctaatagtttagggtaaaaggcaaagccaacaacgtacgttcctaacgatcgatgatctcttcgtggaaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA

Basic information

species Zea mays
transcript GRMZM2G110968_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110968_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g25550.1 (Oryza sativa), 3'ss of exon 2
-----------------gtagggcaggttct-aatagtttagggtaaaaggcaaagccaacaacgtacgttcctaacgatcgatgatctcttcgtggaaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA
                  |        || |  || | | |   | |   | | |   || || | | |  |  | |||| |      |     | |||||   ||| | ||||||| || || ||||||||||| ||  ||| ||||||||||||||| |||| ||||||||| |||||||| || |||||||| |||||||||||
tgccgccttttgctttcatcatctgatttgtcgatgggtcataattagttgtagatgaaataatgcatgaactgatcgattg------tgcaaattgaaactg-cagAGTACTCTGCGTCGCTGCCGTGGTCAACACGCTTGAAGATCGCCATTGGAGCGGCCAGAGGTTTGGCCTTCCTCCATGAAGCTGCCAAGCCCGTCATCTA
















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|76020783|gb|DT947953.1|DT947953
EST:     CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
EST: gi|91049702|gb|EB160120.1|EB160120
EST:     CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
EST: gi|78089532|gb|DV517906.1|DV517906
EST:     GTGTACGAGTTCATGGCCAGGGGCAGC-TGAGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: GTGTACGAGTTCATGGCCAGGGGCAGCTTG-GAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
EST: gi|78089533|gb|DV517907.1|DV517907
EST:     CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
EST: gi|91054554|gb|EB164972.1|EB164972
EST:     CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
EST: gi|67019199|gb|CO447948.1|CO447948
EST:     GGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAA                         GGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG
genomic: CGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAG

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: 5

CACCTTGTCAAGCTCATCGGCTACTGCTACCAGGACGAGCACAGGCTTCTCGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA


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

CACCTTGTCAAGCTCATCGGCTACTGCTACCAGGACGAGCACAGGCTTCTCGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA


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

CACCTTGTCAAGCTCATCGGCTACTGCTACCAGGACGAGCACAGGCTTCTCGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 7

CACCTTGTCAAGCTCATCGGCTACTGCTACCAGGACGAGCACAGGCTTCTCGTGTACGAGTTCATGGCCAGGGGCAGCTTGGAGAAGCATCTCTTCAAAAgtagggcagg ... aaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagccaacaacgtacgttcctaacgatcgatgatctcttcgtggaaacgaacagGGCACTCTGCTTCCCTTCCGTGGTCAACGCGAATGAGGATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTA
                  tcctaac  putative branch site (score: 7)