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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcttgttttctcgaatactaatcaatggttctatttcactgatttgtacctgacttggctttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 17
-----------gtaaattctt--gttttctcgaatactaatca--atggttctattt-cactgatttgtacctgacttggct----ttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG
            |    ||||   |||| |  || |  |||||  ||     | ||| | ||  || | ||     |  |||    ||  |||| | ||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||
gtaagttttctcttgcctctttcattttgtgaaaaaaaaatcatgattaccttgtttgctctctttagaactactgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 14
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 17
-----------gtaaattctt--gttttctcgaatactaatcaatggtt---ctattt-cactgatttgtacctgacttggct----ttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG
            |    ||||   |||| |  || |  ||   ||| ||    | ||| | ||  || | ||     |  |||    ||  |||| | ||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||
gtaagttttctcttgcctctttcattttgtgaaaaaaaaaatcatgattaccttgtttgctctctttagaactactgtcagctcatattgtttttgtttgtcagACATGATTTCCAGTTCTTCAACAACCAAAGGCTCAATGAATTGTATGAAAAGGAAGTCCGGTACCTTATG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 17
gtaaattcttgttttctcgaatactaatcaatggttctatttcactgatttgtacctgacttggctttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG
||||     | |||   |  ||     ||   | || || || |    ||  |        |   |||    | |  | |||| ||||||||||| || || || |  |||||||| ||||| |||||||| || |||||||||||||| |||
gtaagcatctctttgaactgattgctttcttggattgtagttgatgttttcatctgctttatatgttttgcctctgtttttagGCATGATTTCCAATTCTTTAACACACAAAGGCTGAATGAGTTGTATGAGAAAGAAGTGCGGTACCTCATG

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|87155727|gb|DY400516.1|DY400516
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTATATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|32930781|gb|CF035593.1|CF035593
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTATATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|31351381|gb|CD435738.1|CD435738
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|67013537|gb|CO442286.1|CO442286
EST:     GCCTAGGGTAACCAAGGATTCCAATAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTATATGAAAA
genomic: GCCTAGGG-AACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|6194488|gb|AW146592.1|AW146592
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|32930784|gb|CF035596.1|CF035596
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTATATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
EST: gi|6194533|gb|AW146637.1|AW146637
EST:     GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT                         ACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA
genomic: GGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAA

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), 48 (downstream exon)
Score: 394

CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 70

CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 74

CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 73

CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTTgtaaattctt ... tttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggttctatttcactgatttgtacctgacttggctttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG
                                          ttttttgt  CT-rich tract
                                     tttaattttttgtgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcttgttttctcgaatactaatcaatggttctatttcactgatttgtacctgacttggctttaattttttgtgttagACATGATTTCCAGTTTTTCAATAACCAAAGGCTAAATGAATTGTATGAAAAGGAAGTGCGGTACCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA