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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactataatacatgtaaaatatatagttttgtataacatgttgaccaacatatactaattgatatgcatgtgattcatctcttatgacaactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG

Basic information

species Zea mays
transcript GRMZM2G138382_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138382_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g61120.1 (Oryza sativa), 3'ss of exon 6
gtgactataatacatgtaaaatatatagttttgtataacatgttgaccaacatatactaattgatatgcatgtgattcatctcttatgacaac-tcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG
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gtgacga--atattttcagtactcctgttgaaatttcttatggtaaattatgtgtcatgctgaaca---acatgctttatatcctataatatcgtcacagGCTCGTGGTTGTATTCTGGTAGCATCAAGTCCTGAAA-TTCTTACCCGGGTGGAAAAG
















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|32824549|gb|CD964271.1|CD964271
EST:     ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACTG                         GCACGAGGTTGTATTCTCGTGGCATCGAGTCCTG-AAATTCTTACCCGGGT
genomic: ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGT
EST: gi|94473086|gb|EB702044.1|EB702044
EST:     ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAG                         GCACGAGGTTGTATT
genomic: ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATT
EST: gi|211249302|gb|FL028860.1|FL028860
EST:     ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAG                         GCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAA-TTCTTACCCGGGT
genomic: ATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGT

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), 47 (downstream exon)
Score: 56

TTTAAGCCAGCGTTTTGAGAGACGGACATTCGCCGACCCCTTTGAAATCTATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 16

TTTAAGCCAGCGTTTTGAGAGACGGACATTCGCCGACCCCTTTGAAATCTATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG


Block sizes: 38 (upstream exon), 30 (downstream exon)
Score: 3

TTTAAGCCAGCGTTTTGAGAGACGGACATTCGCCGACCCCTTTGAAATCTATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

TTTAAGCCAGCGTTTTGAGAGACGGACATTCGCCGACCCCTTTGAAATCTATCGTGCATTGCGCATCGTAAATCCTAGTCCATATATGGCCTATCTACAGgtgactataa ... caactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccaacatatactaattgatatgcatgtgattcatctcttatgacaactcttagGCACGAGGTTGTATTCTCGTGGCATCGAGTCCTGAAAATTCTTACCCGGGTACAAAAG
                                                ctctt  CT-rich tract
       atatactaattgatat  TA-rich tract