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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattattcttaaactaatggcatacaggtacattttagctgcagcttcaataatttattggcccttttatgtgtaaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG

Basic information

species Zea mays
transcript GRMZM2G078663_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078663_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 8
gtatgtattattcttaaactaatggcatacaggt------acattttagctgcagcttcaataatttattggcccttttatgtgtaaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG
||| |||||  | |  ||| |||| ||| |   |      | |||||   ||| |  | | | | |  |||    |||      | ||||   |||| ||||||||||| |||||||| || ||| | |||||||||||||||||||||||  | ||||| |||
gtaagtatttgtttagaaccaatgacatgctaatctatagatattttcattgc-gtatgactgactc-ttgctgttttcccccttcaaattgtagCTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAG

upper sequence: GRMZM2G078663_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
--gtatgtattattct--taaacta---atggcatacaggtacattt-tagctgcagcttcaataatttattggcccttttatgtgtaaaata---acagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG
   | | ||| | ||   |||| |    |||   |  |  |  |||  |||    |    |||||  || ||  |    | || |  |         ||||||||||| ||||| || ||||| |||||| | |||||||||||||| ||  |||| |  |||   |||
gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG

upper sequence: GRMZM2G078663_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
gtatgtattattcttaaactaatggcatacaggtacattttagctgca--gcttcaataatttattggcccttttatg-tgtaaaata------------acagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG
    ||||   | | || | | |         ||    ||||  || |  | |  ||| ||| |       || |    || | ||||             ||||||||||| ||||| || |||||||||||| | |||||||||||||| || ||||| |  |||   |||
----gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG

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|166625027|gb|EG168088.1|EG168088
EST:     TGAGTAAGGTGTTTGAAGACAGAACATTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTG
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTG
EST: gi|148932104|gb|EC875491.2|EC875491
EST:     TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTT
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTT
EST: gi|50328322|gb|CO523448.1|CO523448
EST:     TGAGTAAGGTGTTTGAGGACAGAACGTTTGTGTCATCTATCCTTAATTCG                         CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCA
genomic: TGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCA

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), 45 (downstream exon)
Score: 488

AGCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 317

AGCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 365

AGCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 350

AGCTCTTCAAATGTCTGTCCAGGATGCAAACATGTCCAGTGACACTGATATGAGTAAGGTGTTTGAAGACAGAACGTTTGTGTCATCTATCCTTAATTCGgtatgtatta ... aaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattttagctgcagcttcaataatttattggcccttttatgtgtaaaataacagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG
                                   ttttatgtgtaaaata  TA-rich tract