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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatccttggtttcatatttgttgtacatggtctatatctcagttggtttgatttttttttctctccacagcatcctgttcttttgggattgaggg...

Basic information

species Zea mays
transcript GRMZM2G095670_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095670_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 5'ss of exon 4
CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcat----ccttggtttcatatttgttgtacatggtctata-tctcagttggtttgatttttttttctctccacagcatcctgttcttttgggattgaggg
 |||||||| ||||||||||||||||||||| | ||| | |||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |  ||    ||   | ||      ||     |||    |||| |||  |   ||||  |    |    | |||||    |  |  |||||  |  ||     
TGATCTTTATTACAGAAGGAAGGAGATATCAAAAGAGTTGTATGAGTTTTGCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGgttagtatttgacccatgatttgcgagtgcccatcattccttatactctgtgcaagtttagtaagatgccttatccaccttgta-taatctttaagacttt----

upper sequence: GRMZM2G095670_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 5'ss of exon 3
CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatccttggtttcatatttgttgtacatggtctatatctcagttggtttgatttttttttctctccacagcatcctgttcttttgggattgaggg
 |||||||| ||||||||||||||||||||| | ||| | |||||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |  || |      | || |    ||||    | | ||   ||  |    |   |  |  |||      |   | |      ||| |   ||      
TGATCTTTATTACAGAAGGAAGGAGATATCAAAAGAGTTGTATGAGTTTTGCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGgttagtattcgacccatgatttgctctgtaagatgcccatcattccttatactctgtgctagtttagtaagatgccttatccaccttgtataatctttaa

upper sequence: GRMZM2G095670_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 5'ss of exon 3
CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatccttg-gtttcatatttgttgtacatggtctatatc--tcagttggtttgatttttttttctctccacagcatcctgttcttttgggattgaggg
 ||||||||| || | ||||| || |||||  ||||||| |||||||||||| | || || || ||||||||||| || || |||||||||||||| |||||     ||      |||   ||| |       |     ||| |   |  ||  |||| ||||   || |       || |  | |  |        |     
TGATCTTTACCACCGGAGGAAAGAAATATCTAAGGAGCTGTATGAGTTCTGCATGGATCAAGGCTATGCAGACCGCAATCTAATTGCAAAGTGGAAGAAGgtttgtttcacaacatttttcattagaatcttctacctcatagcatccctttactttggttttccgtttttgtttgggccttatatgttgacacatctag---

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|71306036|gb|DR789153.1|DR789153
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|7227679|gb|AW566320.1|AW566320
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|71306037|gb|DR789154.1|DR789154
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|7216784|gb|AW562906.1|AW562906
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|78545123|gb|DV622621.1|DV622621
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|78543888|gb|DV621386.1|DV621386
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|33100874|gb|CF060834.1|CF060834
EST:     GCCTGGACCAGGGTTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC

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: 155

CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 79

CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCTTTACTACAGAAGGAAGGAGATATCACAGGAGCTTTATGAGTTCTGCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatccttggtttcatatttgttgtacatggtctatatctcagttggtttgatttttttttctctccacagcatcctgttcttttgggattgaggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA