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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttgctctgcaatacccatgcctttttgattgaactgaactgatctataactatgattgtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATGTTTGTTGAGATAG

Basic information

species Zea mays
transcript GRMZM2G106427_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106427_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g07320.1 (Oryza sativa), 3'ss of exon 3
gtagtttgc---tctgcaatacccatgcctttttgattgaactgaact--gatctataactatgattgtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATGTTTGTTGAGATAG
|||  ||     |     ||     |    || |||     |||   |   |  | ||| | | |||| |||||||| |||| || || |||||||||||||||||||| ||||  ||||| || ||||||||||||||||
gtaccttttctgttgatgattttttttttcttctgaactttctgcttttaaaattctaattcttattgcttgtgaagATTACACTGGAAGCTACTCACCATGGACCAGTCACCAATACACCAACGATGTTTGTTGAGATAG

upper sequence: GRMZM2G106427_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g07320.2 (Oryza sativa), 3'ss of exon 3
gtagtttgc---tctgcaatacccatgcctttttgattgaactgaact--gatctataactatgattgtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATGTTTGTTGAGATAG------------------------------------
|||  ||     |     ||     |    || |||     |||   |   |  | ||| | | |||| |||||||| |||| || || |||||||||||||||||||| ||||  ||||| || ||||||||||||||||                                    
gtaccttttctgttgatgattttttttttcttctgaactttctgcttttaaaattctaattcttattgcttgtgaagATTACACTGGAAGCTACTCACCATGGACCAGTCACCAATACACCAACGATGTTTGTTGAGATAGGTATAGATCTACTTCCATGCTTATATTCTCTGTATT
















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|21432272|gb|BQ547762.1|BQ547762
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|78124578|gb|DV542962.1|DV542962
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76280901|gb|DV020469.1|DV020469
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76280900|gb|DV020468.1|DV020468
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|148935625|gb|EC879669.2|EC879669
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|89764268|gb|DY691136.1|DY691136
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|71772737|gb|DR970664.1|DR970664
EST:     GGTTGATGCAAAAGATAGCCGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|5123996|gb|AI745837.1|AI745837
EST:     CAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: CAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76282654|gb|DV022222.1|DV022222
EST:     GGGTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76017530|gb|DT944700.1|DT944700
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76929934|gb|DV172226.1|DV172226
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|71764615|gb|DR962552.1|DR962552
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76291547|gb|DV031115.1|DV031115
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
EST: gi|76282655|gb|DV022223.1|DV022223
EST:     GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAG                         GTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG
genomic: GGTTGATGCAAAAGATAGCTGTAGAACAAGGCCTTGTTCCAGAGTTTGAGgtagtttgct ... gtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccatgcctttttgattgaactgaactgatctataactatgattgtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATGTTTGTTGAGATAG
                               ctataac  putative branch site (score: 3)
         tttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttgctctgcaatacccatgcctttttgattgaactgaactgatctataactatgattgtttgtgaagGTTACGCTTGAGGCTACTCACCATGGACCAGTTACCAGCACACCCACCATGTTTGTTGAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA