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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttcgttgtagagtattgaacagtggctcctttacatgtttgccctctgctttcttctgaattcctgattgtggctgtactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA

Basic information

species Zea mays
transcript GRMZM2G013079_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 10
gtctgtttcgttgtagagtattgaacagtggctcctttacatgtttgccctctgctttcttctgaattcctgattgtggctg-tactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA
||  ||||| | |     | |||| || ||  ||   |||| | || || | |  |     ||    ||   ||| ||  |   |   | |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||| || ||||||||||| || |||||
gtgcgtttcctcg----atcttgaccaatgcttctcgtacacgctt-ccattttttcatcccttccctctaaattttgaataacaactccgcagATTGCGAGTGGAAAGGACAAGCTGGCAATGTCTGTGTGGCGTCTTTCGATTGGAGCTGCAGCGGCATATGCAAGTCGGTCGAGAGGATCAAGGAAGTACA

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 10
--------------------------------gtctgtttcgttgtagagtattgaacagtggctcctttacatgtttgccctctgctttcttctgaattcctgattgtggctg---tactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA
                                 ||| | |   | |  |||| |  ||      | | | |  | |||      ||  ||    ||||    |     |  |     |  |  || ||||||||||||||| |  ||||| |||||  | ||||| || ||||| || |||||||||||||| || |||||||| || |||| ||||||| |||| ||
gtatggcatctgaaaattctgagaaatacagaatctatatttatttcaagtact--actacaagttcatcatgtattt---tgatgtctttccatgaaacattatacctaaccaaaatgtttgtgtagATTGTGAGTGGAAGGCACAAGCAGGTAACATATGTGTTGCATCCTTTGACTGGAGCTGCAGTGGAATCTGCAAGTCAGTAGAGAAGATCAAATATGTGCA

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G33700.1 (Glycine max), 3'ss of exon 10
gtctgtttcgttgtagagtattgaacagtggctcctttacatgtttgccctctgctttcttctgaattcctgattgtggctg---tactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA
    || | | |   ||  | |||| | |        | ||||| |      ||  |||   ||||    |     |  |     |  |  || ||||||||||||||| |  ||||| |||||  | ||||| || ||||| || |||||||| ||||| || |||||||| || |||| ||||||| |||| ||
----gtatggattctgaaaagtgaaaattctgaaaagttcatgtat-tttggtgtcttcccatgaaacattatacctaaccaacatgtttgtgtagATTGTGAGTGGAAGGCACAAGCAGGTAACATATGTGTTGCATCCTTTGACTGGAGCTGTAGTGGAATCTGCAAGTCGGTAGAGAAGATCAAATATGTGCA

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 10
------gtctgtttcgttgtagagtat-tgaacagtggctcctttacatgtttgccctct------gctttcttctgaattcctgattgtggctgtactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA
      |  | || | || ||   | |    |   |   || | || | || | ||  |       | ||  || ||||  | | ||| ||| |||     | ||||||| |||||||| |  || |||||||||||||||||||| || || ||||||||||||||||| || ||||| || || ||||| ||||||||||| ||
gtacacggttcttccattatattctttactcatcttttttcatgtaaaagtattcctcccaaatggggttctttttgaacacttaattttggttgt-----ttcagATTGCGAGTGGAAGGCACAGGCTGGTAATGTCTGTGTAGCATCATTTGATTGGAGCTGCAGTGGAATTTGCAAATCAGTGGAGAGAATCAAAGATGTTCA

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|211117513|gb|FL479408.1|FL479408
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|71306960|gb|DR789635.1|DR789635
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|60358502|gb|DN225475.1|DN225475
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|5525601|gb|AI861494.1|AI861494
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|60396395|gb|DN229264.1|DN229264
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|60395888|gb|DN228758.1|DN228758
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|60398152|gb|DN230968.1|DN230968
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|5714063|gb|AI944048.1|AI944048
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCCCCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|32940972|gb|CF045791.1|CF045791
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|67018304|gb|CO447053.1|CO447053
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
EST: gi|91869350|gb|EB400347.1|EB400347
EST:     GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCCCCAG                         ATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT
genomic: GGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATT

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: 67

CACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 16

CACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA


Block sizes: 44 (upstream exon), 34 (downstream exon)
Score: 18

CACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA


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

CACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGAACTCCACCAGgtctgtttcg ... actcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtttgccctctgctttcttctgaattcctgattgtggctgtactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA
                             tcctgat  putative branch site (score: 49)
                                            tactcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttcgttgtagagtattgaacagtggctcctttacatgtttgccctctgctttcttctgaattcctgattgtggctgtactcctgcagATTGTGAGTGGAAAGGGCAAGCTGGTAATGTCTGTGTAGCGTCCTTCGATTGGAGCTGCAGTGGCATATGCAAGTCTGTTGAGAGGATCAAAGATGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG