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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtaccttgcctgaggcttaaaagctaacacatgctagtccagttttgatgtgtaccagcctctttctacatactgttacag

Basic information

species Zea mays
transcript GRMZM2G149751_T06
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 5'ss of exon 7
GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtaccttgcctgaggcttaaaagctaacacatgctagtccagttttgatgtg---taccagcctctttctacatac-tgttacag---------
|||||||| |||||||| ||||||||||||||||| ||||  || ||||| |||||||| || || |||||||| ||||||||||||||||||| |      |    || | ||  ||||  |    | |  |  |    |  ||   | ||  || | || || ||  |         
GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtaccttgcgt------ttttggccagcatttgctgatttcatatcaacataacttcacatgtttttcttaaacacatgatattgtttgtgaag

upper sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 8
GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtaccttg---cctgaggcttaaaagctaacacatgctagtccagttttg---atgtgtaccagcctctttctacat-actgttacag
|||||||| ||||||||  |||||||||||||||| ||||  || ||||| |||||||| || || |||||||| |||||||||||||||||      | |||||  |    | |  |     |    |  || |    | | |   |   || |  || ||  ||  | |||
GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtaccttctgtttttaggctgcatgcttgattctattcaacataacttggcctgtttttcttaatatcatgttatattgcttgtgcag
















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|5566727|gb|AI881593.1|AI881593
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211106467|gb|FL269550.1|FL269550
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGCGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|32836434|gb|CD976112.1|CD976112
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|71436763|gb|DR817813.1|DR817813
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|32847674|gb|CD987355.1|CD987355
EST:     CCTCGAGGAAATCCTCAGCCCGTGTGGCCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCGCCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211106464|gb|FL269547.1|FL269547
EST:     CTCGAGGATATCCTCACCCCGTGTGACCAAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAAGGCTCTGACCACCGCCGTGCGACCAACTTTAGTGCC
genomic: CTCGAGGAAATCCTCACCCCGTGTGACCAA-TGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGC-
EST: gi|67018424|gb|CO447173.1|CO447173
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGCGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211107368|gb|FL269551.1|FL269551
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|60396167|gb|DN229036.1|DN229036
EST:     AATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: AATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|60346583|gb|DN213556.1|DN213556
EST:     CTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|18650007|gb|BM498826.1|BM498826
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGCGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|33101475|gb|CF061435.1|CF061435
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211107371|gb|FL269554.1|FL269554
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGAACACCGCCGTGCGACCAACGT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGT
EST: gi|29130233|gb|CB380937.1|CB380937
EST:     CTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|33101251|gb|CF061211.1|CF061211
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|32833047|gb|CD972725.1|CD972725
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|33101222|gb|CF061182.1|CF061182
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|33102528|gb|CF062488.1|CF062488
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|33101156|gb|CF061116.1|CF061116
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211107370|gb|FL269553.1|FL269553
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTC-AGAAGGCT                         GCTGCTGCTCTCAAGG-CTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|211107369|gb|FL269552.1|FL269552
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGCGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|148941572|gb|EC886508.2|EC886508
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
EST: gi|32845718|gb|CD985399.1|CD985399
EST:     CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCT                         GCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT
genomic: CCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtacct ... actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTACTTCGCAGCAAATGCTGCTGCTCAGGCCTCGAGGAAATCCTCACCCCGTGTGACCAATGAAGAAGTCCAGAAGGCTgtaagtaccttgcctgaggcttaaaagctaacacatgctagtccagttttgatgtgtaccagcctctttctacatactgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT