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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgttctaaacttgcttggagatatatcaaaacatttaacgacagcattgaaagttgggatact...

Basic information

species Zea mays
transcript GRMZM2G150867_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 5'ss of exon 5
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgttctaaactt-gcttggagatatatcaaaacat-ttaacgacagcattgaaagttgggatact
||||||||||| || || || ||||||||||| |||||||||||||| || |||||  |||||||||||||||| ||||||||||||||||| ||||||||| ||    | |  |    |  |  | |||| ||| |    |||  ||| |  |   | |   |  ||   | ||  | | | ||||           |   
CCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGATCGTCCTGCTTATGAACAAAAAGTGAAAGgtgatgtggtttaaagccattgaactaattattgtttctgcctagtcttagactattgtttggtttaactgtcttgtccataacattttgccacaaattc--

upper sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 5'ss of exon 5
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattac-tgtcttgttctaaacttgcttggagatatatcaaaacatttaacgacagcattgaaagttgggatact
|| || |||||  | ||||| || || || |||||||| |||||||| || |||||||| |||||||||||||| ||||||||||| |||   || ||||||||  |       | |   || |      |  | ||  | |    ||     ||    | | |       |||           |  | || | | ||| 
CCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGATCGTCCTGCTTATGAGCAACGAGTTAAAGgtaagtcgactcagattctcatgttaagagatatatcaagattctgacaaatctgttagtttctttctctttttcttttatttgcttgatgt-gaggtaca

upper sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 5
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgttctaaacttgcttggagatatatcaaaacatttaacgacagcattgaaagttgggatact
|| ||||||||  | ||||| ||||| || |||||||| ||||| || |||||||| ||||||||||||||||| ||| | |||||||| |  || |||||| | | |||  ||  |  | ||  || ||  |  | |    ||   |  |||   | |   |   |                                 
CCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGATCGTCCTACCTATGAACAGAGAGTTAAAGgttagatattgagt--tgat-tagattcttgttaccctacattatcttatcttcttgctcggtttcag--------------------------------

upper sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 5'ss of exon 5
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgtt---ctaaacttgcttggagatatatcaaaacatttaacgacagcat-tgaaagttgggatact
|| |||||||| || ||||| || || || ||||||||||||||||| || || ||  | ||||||||||| ||  |||||||||||||||  || ||||||| |  || |||| | |   | |    |  |  || || |   ||  |  |||       | |    ||   | || | ||  | | |||  | |   |||  
CCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGACCGAACTGCTTATGAACAAAGAGTTAAAGgtattg-atcatgttcaacattctaaattcccaatcatgcttgccttgaaatgccaatgcctttggttaag-gtctaccaacttcctatgattgctccaata--

upper sequence: GRMZM2G150867_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 5'ss of exon 5
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgttctaaacttgcttggagatatatcaaaacatttaacgacagcattgaaagttgggatact----
|| ||||||||  | || || || || || |||||||| |||||||| || || ||  |||||||||| ||||| ||||||||||||||||  ||||||||||  |  |  |   | ||  | |    |  |  |  |    ||   || ||   |        | | ||  ||| |       |  |||| |   | |     
CCTCAACTTCTTCTCTACCCCAACCCATCAGATCCATTGAATGGAGAGGCTGCAGCCCTGATGATGCGAGATCGGCCTGCTTATGAACAAAGAGTGAAAGgtagca-gtccttctcaagcttcta--gtccccatagtaca-tatgtttactcataaggtggcaagatcaaataatggtgaatcttcaagtggtacttcattca

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|6056913|gb|AW091318.1|AW091318
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|26559982|gb|CA832217.1|CA832217
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAAC
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAAC
EST: gi|67018577|gb|CO447326.1|CO447326
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|211281984|gb|FL018037.1|FL018037
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAA-GGTGAAAG                         AGTACTGTGAAAAATACGCCAAAC-AGAAGATGCTGGGGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|166537158|gb|EG303387.1|EG303387
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAA-GGTGAAAG                         AGTACTGTGAAAA
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAA
EST: gi|12971358|gb|BG267442.1|BG267442
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|211427762|gb|FL233520.1|FL233520
EST:     TGCTTATGAACAAAAGGTGAAAG                         AGTACTGTCAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: TGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|28984207|gb|BQ538996.2|BQ538996
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|15427006|gb|BI542828.1|BI542828
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTCAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|211427761|gb|FL233519.1|FL233519
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|32911041|gb|CF015853.1|CF015853
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTCAAAAATACGCCAAACCAGAGGATGCTGGGGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|5455873|gb|AI833563.1|AI833563
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|5525634|gb|AI861527.1|AI861527
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
EST: gi|166603465|gb|EG175322.1|EG175322
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGC
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGC
EST: gi|211096443|gb|FL454804.1|FL454804
EST:     AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAG                         AGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG
genomic: AGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacatt ... gtttttttagAGTACTGTGAAAAATACGCCAAACCAGAGGATGCTGGTGTCAGCCCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGATCGCCCTGCTTATGAACAAAAGGTGAAAGgtaatacattatgtactagtatatgttattactgtcttgttctaaacttgcttggagatatatcaaaacatttaacgacagcattgaaagttgggatact

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC