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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgtccctcattttgtttcttggaaaatgcag

Basic information

species Zea mays
transcript GRMZM2G092468_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 5'ss of exon 5
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca-actatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgtccctcattttgtttcttggaaaatgcag
|||||||||||||||||||||||||||| ||||||||| |||||||| || ||||||||||| ||||| |||||||| || |||||||||||||||||||||| || ||  | | | | |     ||   || |  |||        ||| | |     |  |  |||    |  |       |   |  | ||||  ||                                                                
GAGATGATGGATCTTATGGATGTGAGCAATGAAATACAGGAAACTCTCGGAAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatcttatttttcagttttcttagattatactggcaccacaaaaatgtttgccttgaagttatgcagtcaacttgttttttctccccacaattct----------------------------------------------------------------

upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G33630.1 (Glycine max), 5'ss of exon 5
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaact-cctttatctctctgctgtccct--cattttgtttcttggaaaatgcag-------------------------------
||||||||||| || |||||||| || | |||||| ||||| ||| | || |||||||| || || || |||||||| |||||||| || |||||||| |||       |   ||| ||| |  ||  ||          |||| ||||  ||   ||  || | ||   |    |   |  ||   |  |   |   |   |  |      ||| |   ||||| | |||   ||   |  |||   || |  |   || | |                                 
GAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGATGAGGATGACCTTATGGGTGgt------tagtaatcttgagatatttgttgg---aaaccattttcaaaaactcc-tagtta-acatggctccacagttggctagggtagtgggattttgtggctgtgatggaaattgtttttatttttctttggttgttgtcatgaagtgtggtttgaattacctgtttctttattttttggttttggtaaaacag

upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G33960.1 (Glycine max), 5'ss of exon 5
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcct---gacacttt-gatttctcttgga---tatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgt----------------------ccctcattttgtttcttggaaaatgcag
||||||||||| || |||||||| || | |||||| ||||| ||| | || |||||||| || || || |||||||| || ||||| || |||||||| |||| | |  || | |  |   ||  |||  ||| | | |||||    |||| ||||  ||   ||  || | ||   |    |   |   |   |  |   |   |   |  |     |||| |  ||| | |   ||   |                       | | ||||| |   || |  ||  |||
GAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATGATCTTATGGGTGgtatgttaaaaatttggttaggaagcttgagatatttgttggaaatcattttcaaaaactcc-tagcta-acatggctccatagttgggcagggtagtgggattttgtggctgtgatgaaaattgttttttgttgttgtcatgaagcggtttgaatgacatgtttctttattttttggttttggtaaaacag

upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 5'ss of exon 5
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgtccctcattttgtttcttggaaaatgcag
|||||||||||||| |||||||| ||  ||||||| |||||| | ||||| || ||||||||  | || |||| | | || ||||| || || ||||| ||||  || |   | |  ||  | |   | ||   |  |||     ||| ||||   ||    |||   | | ||| | |   ||||||  |   |    | | |                                                           
GAGATGATGGATCTGATGGATGTTAGTTCTGAAATTCAAGAATCACTTGGTAGGAGCTACAATATTCCTGATGGCCTTGACGAGGATGACCTCATGGGAGgtaaagtgc--ttgttttgtaattggaagtt---taagat-----caatcgcttgctacgc-tatgcgtctctcatatcatttacattcttttgatatatttcag----------------------------------------------------------

upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 5'ss of exon 5
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatat-atatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatct--ctctgctg-tccctcattttgtttc------ttggaaaatgcag
||||||||||| || |||||||| ||| | ||||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| || || ||||| |||| | || || | |  | | |  |         |||||         | ||||     || |   || || ||||     | | | |||  || | | | |  || | |      | ||||  | |   | |   | |   |  |||| | ||      ||      |||||
GAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATGACCTCATGGGCGgtatgcttaaattgtattcatatgtcatggaactttgga-----atggatgctaagagaatgttgcattttcttcagtatccttgc-ttgtcacgagggtcagcaaagggttctccccccttcttttaattttatagatttattgttttatgtccctcttttttcccctgcag

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|37622046|gb|CF675099.1|CF675099
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGC
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGC
EST: gi|211387542|gb|FL169282.1|FL169282
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGTAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|211394823|gb|FL369347.1|FL369347
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|24934372|gb|CA452590.1|CA452590
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|17932462|gb|BM269422.1|BM269422
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|32908604|gb|CF013417.1|CF013417
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACAT
EST: gi|32844108|gb|CD983789.1|CD983789
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|18170299|gb|BM340139.1|BM340139
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|32844472|gb|CD984153.1|CD984153
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|32916309|gb|CF021121.1|CF021121
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|32850682|gb|CD990363.1|CD990363
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|4609483|gb|AI600322.1|AI600322
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|76286967|gb|DV026535.1|DV026535
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|17929488|gb|BM266448.1|BM266448
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
EST: gi|87151661|gb|DY396450.1|DY396450
EST:     CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGG                         AGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT
genomic: CAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttca ... gaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAGAACTTATGGGGGgtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgtccctcattttgtttcttggaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC