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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta...

Basic information

species Zea mays
transcript GRMZM2G009843_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g53720.1 (Oryza sativa), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattt-tttcacatcgccctgtttt-catctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta-
|||||||||| ||||||||||||||||||| |||||||||||| |||| || ||||||||||||||||| |||||||| || | || |||||| |||||||||||||||||| ||||    |      |||   ||||||   |   || |   || ||   ||  |  || |    ||    | |    ||||  ||| || 
ATCTGCTGACTTGTGGTCCTTTGCATGCATATGCTTTGAGCTTGCCACAGGAGATGTGCTATTTGATCCGCACAGTGGTGACAGTTATGACAGGGATGAGgtatgtctatttatttctttccaagacatttcatatctatacaaaacttaactcaaactatcacctgtcaacactttagc---ttaaaaaaataggagtctat

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G08900.1 (Glycine max), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta-----
  |||| ||  | ||||||||||| ||||||||||| |||||| ||||||| ||||| || |||||||| |||||||| || || | ||| ||||||||||||   | ||   | |||   |   |||  | |      |   | |||     |  || | | |  ||  |  |     |  | | | | ||  | || |     
CCCTGCAGATTTATGGTCCTTTGCTTGCATTTGCTTCGAGCTTGCCACTGGTGATGTTCTTTTTGATCCTCACAGTGGTGACAACTATGATAGAGATGAGgtaa--ccataactgcac-ctgttttgtactaaaaagaagctat-ttggctttattttgtgctattaagtatcaccaccatgcttacaactatta-tgaacttgt

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G30440.1 (Glycine max), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttc--acatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta
  | || ||  ||||||||||||| |||||||||||||||||| || |||| ||||| || |||||||| || ||||| || || | ||| || ||||||||| ||  |  | ||   || | |      ||   |   ||    | ||| |  || ||| || | |         || |  || |||   ||     | | 
TCCAGCAGATCTGTGGTCCTTTGCTTGCATTTGCTTTGAGCTTGCCTCTGGCGATGTTCTTTTTGATCCTCATAGTGGTGACAACTATGATAGGGATGAGgtaagtgcacctgtttggactttgaaagaattggttggcttcatttcttgctctaatcttcta-atgtttgctgttaatattattattatcattattattt-

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G21320.1 (Glycine max), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctatttt-ttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaata--caagtgta
 ||||| ||  | ||||| ||||| |||||||| ||||||||| | ||||| |||||| |||||||||| |||||||| || || ||||| || |||||||||||| |||||| || || ||    | | ||   |||    |   ||  |    | | |    | ||    ||     |      | || |   |||    |
GTCTGCAGATCTTTGGTCTTTTGCTTGCATTTGTTTTGAGCTTGCAACTGGAGATGTGTTATTTGATCCTCACAGTGGTGAGAACTTTGATAGGGATGAGgtatgtgtattttgtttacttctttatatgtt---ctacctgatcatttttactccatgaagtgaaaattttaggttccatggtccttgatttttcaaaaaga

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G07430.2 (Glycine max), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaat--acaagtgta-
|||||| ||  | ||||||||||| |||||||| ||||||||| | ||||| |||||  |||||||||| |||||||| || || ||||| || |||||||||||| |||||| |   ||     | | | | ||||    |   ||  |    ||| |    | ||    ||            | || |   |||    | 
ATCTGCAGATCTTTGGTCCTTTGCTTGCATTTGTTTTGAGCTTGCAACTGGAGATGTATTATTTGATCCTCACAGTGGTGACAACTTTGATAGGGATGAGgtatgtgtattttgtttaattatt-tatatgc-tctacctgatcattc-taattcctgaagtgaaaattttaggttctgtggtccttgattttgcaaagagaa

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G05480.1 (Glycine max), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgc-------cctgtt---ttcatctattgtactgttgatgg---aaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta
  | || ||  ||||||||||||| |||||||||||||||||| |  |||| ||||| || |||||||| || ||||| || || | ||| || ||||||||| ||  |  | || | |             ||||   ||||| |||||  ||  | ||     ||  ||       || |  |  || || || |||              
TCCAGCAGATCTGTGGTCCTTTGCTTGCATTTGCTTTGAGCTTGCATCTGGTGATGTTCTTTTTGATCCTCATAGTGGTGACAACTATGATAGGGATGAGgtaagtgcacctgtttagactttgaaagaatttgttggcttcatttattgctctaataatcatctaatgtttgctgttaatattaataataatattattt-------------

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G53030.1 (Arabidopsis thaliana), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtcta------------ttttttcacatcgccct------gttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaata--caagtgta------------------------------------
|||||| ||  | ||||| || || ||||| || ||||| |||  |||||| ||||||||||||||||| || |||||||| |||| ||| ||||||||||||||  ||            | ||||  |   |  |       ||||| |  |||| |    ||       | |  |    |  |           | |   |  |||   | | |||                                     
ATCTGCAGATCTCTGGTCATTCGCGTGCATATGTTTTGAACTTGTCACTGGAGATGTGCTATTTGATCCCCATAGTGGCGACAATTATGATAGAGATGAGgtatgcttaagttccctgctgtcttttggctgtgtgcatttgtggtttttacatattttggctttctcttctcttgttttgtgggatcttagcgtggatttgcttcaattttctattgtgggagtttggaaatctaattggcttttctgttaacag

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttat-acaagaaaaaaagaaagaaaatcattcgaatacaagtgta
 ||||| || |||||||||||||| || ||||| || |||||  |||| || |||||  | || ||||| |||||||| || |||| |||| | ||||||||||||  || | |     || |  | ||| |   | | |||          |    ||| || |  |            ||    | |  |     |   
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatat---tcactttctttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G22840.1 (Arabidopsis thaliana), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccc-tgttttcatctattgtactgttgatgga-accttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta
 || || || |||||||| ||||| |||||||| ||||||||| |||| || ||||| ||||| ||||| |||||||| || || |||||  |||||||||||| | | | || |   ||  | | |  |||     |   ||   | | |  |   | | |  |   ||     | |  ||   | |    |   ||    
CTCAGCGGATATGTGGTCATTTGCTTGCATTTGTTTTGAGCTTGCCACCGGAGATGTTCTATTCGATCCTCACAGTGGTGAAAACTTTGAGCGAGATGAGgtatatatctcttatgtgatttctcatactttgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcag----

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0061g01050.t01 (Vitis vinifera), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaataca-agtgta--
 || |||||  | ||||||||||| |||||||| ||||||||    ||||| ||||| || |||||||| |||||||| || || | ||| || ||||||||||||  |  |  | |  |     || ||       ||| | ||   ||      |      ||||   |      || ||| ||  |  ||  | ||    
TTCAGCTGATCTATGGTCCTTTGCTTGCATTTGTTTTGAGCTGGTAACTGGAGATGTTCTTTTTGATCCTCACAGTGGTGACAACTATGATAGGGATGAGgtatgtagagatccttaattt---ttgcttgtggaccttggaatgcctatttttagtgtccatagaactgactttctaacatctttttaccacttattgctat

upper sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g04220.t01 (Vitis vinifera), 5'ss of exon 2
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta-----
 ||||| ||  | ||||||||||| |||||||| ||||||||| | ||||| ||||| || || ||||| |||||||| || || ||||| ||||||||||||||  ||  ||||    |     | || | |   ||| || |||| |||   |         |   || | |     | || ||  |||       ||     
TTCTGCAGATCTTTGGTCCTTTGCTTGCATTTGTTTTGAGCTTGCAACTGGTGATGTTCTCTTCGATCCTCACAGTGGTGACAACTTTGATAGAGATGAGgtatggatacgtttttttgttttttttttgtgaa--attatattgtttatgatgct---cgtgtgctgaatatatcttgattctttgaaatcggtccttatttct

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|22543237|gb|BU093675.1|BU093675
EST:     GGTATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCACTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
EST: gi|21760117|gb|BQ635658.1|BQ635658
EST:     GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCACTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
EST: gi|26457617|gb|CA829200.1|CA829200
EST:     GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCACTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
EST: gi|26457145|gb|CA828728.1|CA828728
EST:     GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCACTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
EST: gi|33093528|gb|CF053522.1|CF053522
EST:     GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
EST: gi|22473236|gb|BU037716.1|BU037716
EST:     GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAG                         GATCACCTTGCACTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG
genomic: GGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctat ... tgtaatgcagGATCACCTTGCGCTGATGATGGAACTGCTAGGAATGATGCCTCGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttatacaagaaaaaaagaaagaaaatcattcgaatacaagtgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaaa