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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG

Basic information

species Zea mays
transcript GRMZM2G070045_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 19
tctgtcaatttagtttatcgaatttaaacattaac--actctagagtttgcttataatagttgtcttaatgtgctttagtttaatact-----gtttgtgtgtg-tagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
        | |   || | | || |||||  | ||  | ||  ||   |  |||     ||| ||||  | | ||| | || || |||     || | | | |  ||| |||||||||||||||||||||||||||||||||||||||||| | ||| ||||||||||||| || ||||| ||||||||| |||||
-------gtgttccttgtggcatgtaaacggtcacttattcctgataatagttagtcatgtt-tctttctatacttgatttgaagacttccgggtctattttttctagATATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCCTGGAGCAAACAATTGTGGTATACGTTGATCATCTCCTTACTCAG

upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
tctgtcaatttag-tttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
   || | |||   |||  |   |||    |  || |  | | | |       ||  |||    | ||  ||   | ||  |||||||        || |||||| | ||||||||||||||| |||||||||| || || ||  | || |||||| | || ||||||||||||||||||||  |||||
---gtaagtttttctttcccccttttgtttaacaagagccaaaaatgc-----tacaagtctattgaagatgtcgtggtg-aatactgg------atgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG

upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 20
tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaa-------tgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
      | |||  |  ||| |   |    ||  ||  |   | || |  || | ||| ||   ||||       | |  |||| | ||| |   ||||||     ||||| |||||||||||||||||| | |||||||| || |||||| | || |||||  | || || |||||||| || |||||  | |||
-----aagtttgctgaatccagcctgttgatctacttttctgtgtctcattttcatatttaagttaaaaacatctcttatttactctaa-atcttttgtg-acaaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG

upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtctt---aatgtgcttta---gtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
      | |||  |  ||| |   |    ||  ||  |   | || |  ||   ||| ||   ||   ||  |   |||   | |  | |   ||||||  |  ||||| |||||||||||||||||| | |||||||| || |||||| | || |||||  | || || |||||||| || |||||  | |||
-----aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgacta-agGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG

upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ12004 (Selaginella moellendorffii), 3'ss of exon 19
tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
                                                    | | |   |  ||||  | |   | |||   | |||  |||| || ||||||||||| || ||||| |||||||| ||||  ||||||||  ||||||| ||||||||  | || || || ||||||||| | |||
---------------------------------------------------gtgagacacga-ttaacctacccgacttt--caatgtgcgtgt-tgcagGTATATTGAGGACAGATCGTTTCGAAGGTTTGCTGAGGCTTGTCTAGAGGAGACAATTGTCATATACGTGGATCATCTCCTTACACAG

upper sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ08885 (Selaginella moellendorffii), 3'ss of exon 19
tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgct-ttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
                                                    | | |   |  | |  | |||    |  |   | |||  || | || ||||||||||| || ||||| |||||||| ||||  ||||||||  ||||||| ||||||||  | || || || ||||||||| | |||
---------------------------------------------------gtgagacacgattaaccgagctacccgactttcaatgtgcgttt-tgcagGTATATTGAGGACAGATCGTTTCGAAGGTTTGCCGAGGCTTGTCTAGAGGAGACAATTGTCATATACGTGGATCATCTCCTTACACAG

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|60398228|gb|DN231044.1|DN231044
EST:     ATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAAT                         GTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
genomic: ATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
EST: gi|67037440|gb|CO464256.1|CO464256
EST:     CAGAATATCTTGTCGCAACATTTGCTGATTACTTTGNGTGATGT-AAAAT                         GTATATTGAAGAA-GATCATTTCGAAGATT-GTGGAGGCTTGCATAGAAGA
genomic: CAGAATATCTTGTCGCAACATTTGCTGATTACTTTG-GTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
EST: gi|67016798|gb|CO445547.1|CO445547
EST:     ACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAAT                         GTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
genomic: ACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
EST: gi|24934258|gb|CA452476.1|CA452476
EST:     ACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAAT                         GTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
genomic: ACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGA
EST: gi|24934377|gb|CA452595.1|CA452595
EST:     ACAGAATATCTTGTCGC-ACATTTGCTGATTACTTTGGTGATGTTAAAAT                         GTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCAT
genomic: ACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 283

ACTGGCTGGAGGGAATGGTCACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 279

ACTGGCTGGAGGGAATGGTCACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 243

ACTGGCTGGAGGGAATGGTCACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 404

ACTGGCTGGAGGGAATGGTCACAGAATATCTTGTCGCAACATTTGCTGATTACTTTGGTGATGTTAAAATgtaagcttta ... gtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
                           tttagtttaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtcttaatgtgctttagtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttt