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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCCGCAACGTCAGACATTGATGTTCTCTGCAACAATGCCAACATGGATACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaacttctagtgttactgttgtttatgcacatttattgcttgacttctcaacttgaattacgatggacttgtttatattgcatatttttgtat...

Basic information

species Zea mays
transcript GRMZM2G107984_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107984_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 5'ss of exon 3
GCCTCCGCAACGTCAGACATTGATGTTCTCTGCAACAATGCCAACATGGATACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaacttctagtg-------ttactgttgtttatgcac---atttattgcttgacttctcaacttgaattacgatggacttgtttatattgcatatttttgtat
 |||||  ||||||| || |||||||||||||| || |||||||| ||||| | ||  ||||| ||||| ||||| || |||||||| ||| ||||||||||||||   |    |  |        || || ||| || | |||   ||  ||||| |   || |  |  |  ||     ||   || |||| | ||||   |       
ACCTCCAAAACGTCAAACCTTGATGTTCTCTGCGACTATGCCAACTTGGATTCAGAGACTCACCCAGAAATACCTTAAGAATCCTGTTACAATTGACCTTgtgagttttatacttgctaaactcctttgctcttggttttacacataatccattgcatagattgtggaactatatc----tgtttttatttaaaatgcactctc------

upper sequence: GRMZM2G107984_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 5'ss of exon 3
GCCTCCGCAACGTCAGACATTGATGTTCTCTGCAACAATGCCAACATGGATACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgca-acttctagtgttactgttgtttatgcac-------atttattgcttgacttctc-aacttgaattacgatg-gacttgtttata-ttgcat-atttttgtat----------------------------------
||| |   | |||||||   ||||||||||||||||||||||||  |||||  ||||||| || ||||||||||| || |||||  | ||  |||| |||||||||    |    | || || |  ||  |||| | |       | | | |  |   ||| || ||  |  |||| ||   | | ||||  ||  |   | ||| || |                                    
GCCACAAAATCGTCAGAGCATGATGTTCTCTGCAACAATGCCAAGTTGGATTAGGAAGCTTACCCAGAAGTACCTAAAAAATCCATTAACTATTGATCTTgtgagtttggagagtttgtttttccatttcttattcgctggttgtagtaactattatccttttccaagctatattatgaaaaggcatgttcttaactatttgattcttatgactgcaaacttattaatattggatgttcactgtag
















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|32838568|gb|CD978246.1|CD978246
EST:     TACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|60337954|gb|DN204927.1|DN204927
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|91056824|gb|EB167242.1|EB167242
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|87152778|gb|DY397567.1|DY397567
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|149061229|gb|EE157494.2|EE157494
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|32837236|gb|CD976914.1|CD976914
EST:     CCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: CCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|78113910|gb|DV532299.1|DV532299
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|149089755|gb|EE179029.2|EE179029
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|32836838|gb|CD976516.1|CD976516
EST:     ACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: ACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|32839302|gb|CD978983.1|CD978983
EST:     ACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: ACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|71304548|gb|DR788393.1|DR788393
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|32837093|gb|CD976771.1|CD976771
EST:     ACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: ACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
EST: gi|19855082|gb|BQ060134.1|BQ060134
EST:     TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTT                         GTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC
genomic: TACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaa ... ttctttctagGTTGGTGAGGATGACCAGAAGCTTGCTGAAGGAATTAGTCTTCTCGCTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCCGCAACGTCAGACATTGATGTTCTCTGCAACAATGCCAACATGGATACGGAAGCTCACACAGAAGTACCTCAACAATCCTGTCACAGTTGACCTTgtgagtgcaacttctagtgttactgttgtttatgcacatttattgcttgacttctcaacttgaattacgatggacttgtttatattgcatatttttgtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT