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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_T01
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|78543888|gb|DV621386.1|DV621386
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
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|60359481|gb|DN226454.1|DN226454
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|211218105|gb|FL085264.1|FL085264
EST:     GCCTAGACCAGGGTTATGCAGACCGYAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCG
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCG
EST: gi|71306037|gb|DR789154.1|DR789154
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|78545123|gb|DV622621.1|DV622621
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|7216784|gb|AW562906.1|AW562906
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|211218104|gb|FL085263.1|FL085263
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGT
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGT
EST: gi|78544043|gb|DV621541.1|DV621541
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|60394589|gb|DN227459.1|DN227459
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAGACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|19822372|gb|BQ048396.1|BQ048396
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|211215545|gb|FL085259.1|FL085259
EST:     GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGC-TTTGCTGCCTCCGGTGCATACAGACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
EST: gi|33100874|gb|CF060834.1|CF060834
EST:     GCCTGGACCAGGGTTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC
genomic: GCCTAGACCAGGGTTATGCAGACCGTAACCTGATTGCAAAGTGGAAAAAGgtaatcatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCAC

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