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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttggattctatataatagcaatgttttcttcttcctaaatcttgacagatcactaacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 3'ss of exon 11
gcaagttggattctatataatagcaatgttttcttcttcctaaatcttgacagatcactaacgtgccca--tttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT
| ||| || ||    | |    | |     |||       |   |||  |  |    ||||  | |||   ||| || |||||||||||||||||||| || || || || ||||| |||||||||||||||||||| || ||||||||||| ||||| |||||||| ||||||||| |||| |
gtaagatgaatatcctgttgccgaacatcattccatgggatgtttctgaatggcatgctaagtttccctgcttttaccttgcagTTGATCAACCCAGAGGTTACCGTCACAATGACTGAGAACACTCCTGATGATCCTCGTCAGAGGAAGCCAGACATTACAAAGGCAAAGGAAGTTTTGGGGT

upper sequence: GRMZM2G165357_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------------------------gcaagttggattc-tatataatagcaatgttttcttcttcctaaatcttgacagatcact----aacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT
                                                                    |||      ||| |  ||| |     ||      |      |||||||  ||  |   |    || ||           ||||||| | || || |||| ||||    | | ||||   |||||||||||||||||||| || || || || || ||||||||||| || |||||| |  |||| |
gtcagttttaagcatctttaaatataattgagctatttttcttaaggtggattgcatgttcagtgtaccaaaccaatttcatccatatttatgttgaaagtgtgaatgaaaatcttttcaagtttttgtttaatgttttgtgggtggtttgcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGATCCGCGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT

upper sequence: GRMZM2G165357_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 10
--gcaagttggattctatataatagcaatgttttcttcttcctaaatcttga-cagatcactaacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT
  |  |||  | ||       ||   |    |   | |||   || |||||        | | |  ||    ||||   |||||| |||| |||||     |     | | ||||   |||||||| || ||||||||  | ||||||||||| |||||||||||||| || |||||  ||||||
gtgagagtctggtttctcgatatgatatgagtaagtacttagaaattcttgggtccgctaatgaaatgttggttta--cttgcagCTGATTAACCCGAGCATAGAGATAAAGATGGTTGAGAACACACCGGATGATCCAAGACAGAGGAAGCCAGACATCACAAAGGCTAAAGAAGTGTTGGGAT

upper sequence: GRMZM2G165357_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 12
--------------------------------------------------------------------------------------------------------------------gcaagttggattctatataatagcaatgttttcttcttcctaaatcttgacagatcactaacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT
                                                                                                                      || ||  |||  | || ||   ||| |       ||          |    |  |||   | |   | || |   ||||| | ||||||||  | ||     | |  |||   || ||||| || || ||||| |||||||||||||| |||||||||||||| |||||  | |||||||
gtgagtactatatttgcctctttttttcttttttaattagcaatatctggttcctttggcccaaattaaatccatcttctctgcaatttccaaacattaccatgagatataaaagcaaaaattatattaaaaatcatgagaatatgaaagatttggatgtggcagctctaatacttg-gagattaattgaacatgcagCTTATCAACCCTAAGGTTGAGATCAGCATGGTGGAAAACACACCAGACGATCCTCGCCAGAGGAAGCCAGACATCACAAAGGCAAAGGAGTTGCTGGGAT

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|18176493|gb|BM351426.1|BM351426
EST:     AATGTGAAGGAG                         TTGATCAACCCAGATGTGGCAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: AATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18169307|gb|BM339147.1|BM339147
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|16922387|gb|BM075557.1|BM075557
EST:     TGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: TGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|13562266|gb|BG550486.1|BG550486
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|13558126|gb|BG549482.1|BG549482
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|5525817|gb|AI861710.1|AI861710
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|5871227|gb|AW017698.1|AW017698
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18168819|gb|BM338659.1|BM338659
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18172685|gb|BM348073.1|BM348073
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|149070502|gb|EE158906.2|EE158906
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|71444249|gb|DR825299.1|DR825299
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|211023433|gb|FL440281.1|FL440281
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTG
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTG
EST: gi|6012581|gb|AW062018.1|AW062018
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACAATGACCGAGAACACTCCTGATGAC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|211023434|gb|FL440282.1|FL440282
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATNGTGACAGTGACGATGACCGAGAACACTCCTGATGA
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGAT-GTGACAGTGACGATGACCGAGAACACTCCTGATGA
EST: gi|32848833|gb|CD988514.1|CD988514
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18164214|gb|BM334053.1|BM334053
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|60342197|gb|DN209170.1|DN209170
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|32864569|gb|CF004251.1|CF004251
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|71449952|gb|DR831002.1|DR831002
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|211225103|gb|FL464256.1|FL464256
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|14243914|gb|BG841625.2|BG841625
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|32850797|gb|CD990478.1|CD990478
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|149082964|gb|EE172200.2|EE172200
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18166053|gb|BM335892.1|BM335892
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18171739|gb|BM341579.1|BM341579
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18174516|gb|BM349904.1|BM349904
EST:     TGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: TGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|149065531|gb|EE286651.2|EE286651
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCC
EST: gi|18173577|gb|BM348965.1|BM348965
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18171489|gb|BM341329.1|BM341329
EST:     GGAACCCAGGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGGACACTCCTGATGAT
genomic: GGAACCCAGGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|18176777|gb|BM351710.1|BM351710
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|45213764|gb|CK850000.1|CK850000
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|5847454|gb|AW000533.1|AW000533
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcttcttcctaaatcttgacagatcactaacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT
                                         atttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttggattctatataatagcaatgttttcttcttcctaaatcttgacagatcactaacgtgcccatttaactttgcagTTGATCAACCCAGATGTGACAGTGACGATGACCGAGAACACTCCTGATGATCCCCGCCAGAGGAAGCCGGACATCACAAAGGCGAAGGAAGTTCTGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA