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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgctctgctgattcatcttatgttcgacgtgagaaaagaagatgttgagccaaatgaaatgagtgaccgcttccttctgcttgctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA

Basic information

species Zea mays
transcript GRMZM2G132069_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 8
gtacgtacgctctgctgattcatcttatgttcgacgtgagaaaagaagatgttga-gccaaatgaaatgagtgaccgcttccttctgcttgctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
    ||| | | |  | ||||  ||| |      | |     ||      ||  | ||  ||| | |||  ||| |   |  ||        | | |||||| |||||||||||||| ||||| || ||||| || ||||| || || || |||||||| ||  |||||| ||||||||||||||| || || |||||||
----gtatgttttaatcattctacttgttcattgcattgatcaatctagggtaaatgctgaattatatggttgatctacttttt--------tacttcagGATTGTTGCTTAATCCCAGAGTCTCCATTCTATCTAGAAGGAAAAGGTGGACTCCTTGAATTCATCGAGAAACGGCTCAAGGACAATGGCCATATGGTCA

upper sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 8
---------------------------------------gtacgtacgctctgctgattcatcttatgttcg-acgtgagaaaagaagatgttgagccaaatgaaatg--agtgaccgcttccttctgcttgctgcctca-gGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
                                        | | |  |     |||  || | || | |||    || |  |   |   | |     ||  |   ||   | ||   ||  |  | |||| || |      |||||||||||| || || ||||| ||||||||||||||||| ||||| || ||  ||||                                         
taacaattgtaagtgtattttatcgtctaagtgcaccagttgcttttgaggatctggatctttttcttttcctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATGCCACTCT-TGCTAGCAGAGATGTGGACTGTTGCTTGATTCCAGAGTCACCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA-----------------------------------------

upper sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 9
------------------------------------gtacgtacgctctgctgattcatcttatgttcgacgtgagaaaagaaga-tgttgagccaaatgaaatgagtg-accgcttcc---ttctgcttgctgcctca-gGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
                                     | | |  |     |||  || | || | |||    || |  | || || |  |  | |    |   | | || |  |  | |   |  |||| || |   |  |||||||||||| || || ||||||||||||||||||||||| ||||| || ||  ||||                                         
caattgtaagtgtattttatcctctaagtgcaccagttgcttttgaggatctggatctttttcttttctttctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATGCCACTCTTGCTAGCAGAGACGTGGACTGTTGCTTGATTCCAGAGTCGCCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA-----------------------------------------

upper sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
----------------------------------------------gtacgtacgctctgct--gattcatcttatgttcgacgtgagaaaagaagatgttgagccaaatgaaatgagtgaccgcttccttctgcttgctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
                                              ||    |  ||   ||  | ||||| | ||| |  |  |  | |   | ||||  |     | || ||||  ||  |    | | |   | |   | |  ||||||||||||||| || ||||| ||||| ||||||||||| |  || || |||  |||                                         
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatat-atgctttat-tttggatttatgatgcagGATTTATTGCAATGTATG--CTACACTTGCAAGTCGAGACGT--GGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA-----------------------------------------

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|149085166|gb|EE174669.2|EE174669
EST:     ACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTG                         GACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
genomic: ACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
EST: gi|78076659|gb|DV505093.1|DV505093
EST:     AACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTG                         GACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
genomic: AACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
EST: gi|78088953|gb|DV517346.1|DV517346
EST:     CAACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTG                         GACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
genomic: CAACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
EST: gi|74233713|gb|DT641627.1|DT641627
EST:     CAACAGCGGTTTCATTGTCATGTTCGCTACTCTAGCTAGCCGCGACGTG                         GACTGTTGCTTAATCCCGGAGTCGCCCTTCTACC-TGAAAGGGAAGGGAGG
genomic: CAACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTG-AAGGGAAGGGAGG
EST: gi|71315899|gb|DR794637.1|DR794637
EST:     CAACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTG                         GACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG
genomic: CAACAGCGGTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGG

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: 32 (upstream exon), 40 (downstream exon)
Score: 5

GTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 60

GTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

GTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 47

GTTTCATTGCCATGTACGCTACTCTAGCTAGCCGCGACGTGgtacgtacgc ... gctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagatgttgagccaaatgaaatgagtgaccgcttccttctgcttgctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
                                cttccttctgcttgct  CT-rich tract
              aaatgaaat  TA-rich tract