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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtatttttttttactttgtttatttagattagagtcagctttgatgcttatagtttgaggggaatagacaatggaacgcgacagactaaggtcttt...

Basic information

species Zea mays
transcript GRMZM2G472625_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtatttttt--tttactttgtttatttagattagagtcagctttgatgcttatagtttgaggggaatagacaatggaacgcgacagactaaggtcttt--
||||||||||||||||||||||| |||||||| ||||||||||||||||| || || ||||| |||||||| |||||| ||||||||||| || |||  ||| ||| ||||   || ||||     |  | |  || ||    |  | |        |  ||      | |  || |    | |||  
ATTTTCCACAAGAGAATGCCTCCAGAAGCCATAGACCTTGCTTCCCGTCTTCTCCAATATTCACCAAGTCTACGCTGCACTGCTgtgagttttctttcgtttgcttagttt---tatattatctataaatctattgttttcgctaagcgctaggataatgattatttac-atggatttgcttatttta

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA12G15470.1 (Glycine max), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagta---------------tttttttttactttgtttatttagattagagtcagctttgat--gcttatagtttgaggggaatagacaatggaacgcgaca----gactaaggtcttt-------------------------------------------------------------------
 ||||||||||| |||||||||| ||||| ||||||||||| ||  | || || || ||||| || ||||| |||||| |||| |||||||                 |   || |||||     |||| || | ||  |    |     |   | ||||||       ||  |        | || |      |||   || ||                                                                   
GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCGgtgagtaggatgaactatgatacctcccttcacttttcccctttaaataaaaggaaaacatacacaggaaaaagtttgcttattttaaccttcttgctgtgatattatatctatattccttatggcatgttttttaatttagttaactcaattggcttaattttcactggtggcttttattatttcag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagta---------------tttttttttactttgtttatttagattagagtcagctttg---atgcttatagtttgaggggaatagac--aatggaacgcgacagactaaggtcttt--------------------------------------------------------------------
 ||||||||||| |||||||||| ||||| ||||||||||| ||  | || || || ||||| || ||||| |||||| |||| |||||||                 |   || ||||      |||| || | ||  |    |    | |   |   ||||     | ||  |    ||  |    | |  |||   || ||                                                                    
GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCGgtgagtaggatgagccatgatacctaccttcacttatcccctttaaataaaaggaaaacatacacaggaagaagttttgcttatattaaccttgctgtgatattatat-ctatattccttatggcatgttttttttatttagttaactcaattggcataattttcaccaatggcttttattatttcag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattttt-------ttttactttgtttatttagattagagtcagctttgatgcttatagtttgaggggaatagacaatg-gaacgcgacagactaaggtcttt----------------------------------------------------
|| |||||  | | ||||||||| ||||| || || ||||||||||| || || |||||||| ||||||||||| ||  |||| ||||||    ||       ||||  ||| ||| | |   |   | |||  |    |   |  |   ||    | |||     |  ||| |  |  |  ||  | || |                                                    
ATATTCCATGAAAAAATGCCTCCAGAAGCAATAGATCTTGCTTCCCGGCTTCTGCAGTATTCCCCAAGTCTTCGATGTACTGCGgtgagtgcgattgctgcaattttgatttatttgtctgtgtggaactcatttagtctttcttcaacgtggccagtatatttcttctgaatgttatcggttacagactgttacatatattaactagcatagcagcttgaggaggattttctttgttatgcag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtatttttttt-----tactttgtttatttagattaga-------gtcagctttgatgcttata--gtt---tgaggggaatagacaatggaacgcgacagactaaggtcttt-----------
 ||||||||||| | |||||||||||||||||||||||||| || || || ||||| || || |||||||| || ||| |||| ||  |||||| |        |||| |   |  ||| | | |        | |  |||||   | || |  |||   ||| ||    | |   ||     | || ||||    | |||           
GTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCGgttggtatttctaaaccaagtactcttaattgttacagtggttctctctggcttctttggaccatacactgttcaatgaaggagtgaaatgttgtttttcaactgacttgtttgtttgccgtctgaag

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 10
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtatttttttttactttg-tttatttagat-tagagtcagctttgatgcttatagtttgaggggaatagacaatgg---aacgcgacagactaaggtcttt
 | || |||||  |||||||||| ||||| || || |||||||| || || || || || || ||||||||||||||| | |||||||||  ||  || | || ||  || | ||||| ||  || |  | || |  | |||||||  |     |  |  | |    |  | |   ||||||   ||| 
GTCTTTCACAAACGAATGCCTCCTGAAGCAATCGATCTTGCTTCTCGACTTCTGCAATACTCACCAAGTCTTCGCTGCACAGCTgtgagt--ttgattctgctatgacttttctagatatatggttacatatggt--tgatagtttaggaaactttcatgaggactcattgaggttgactaattactt-

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|22472814|gb|BU037294.1|BU037294
EST:     CCTTCAGTATTCGCCAAGTTTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: CCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|32907164|gb|CF011977.1|CF011977
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCCTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|211080741|gb|FL326809.1|FL326809
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|60338769|gb|DN205742.1|DN205742
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|60341112|gb|DN208085.1|DN208085
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|149087811|gb|EE287133.2|EE287133
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|71760137|gb|DR958074.1|DR958074
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|211442652|gb|FL343508.1|FL343508
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|60351318|gb|DN218291.1|DN218291
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|211096380|gb|FL340966.1|FL340966
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|211467509|gb|FL214418.1|FL214418
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTT
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTT
EST: gi|110210635|gb|EC892532.1|EC892532
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|22472815|gb|BU037295.1|BU037295
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|166542190|gb|EG255599.1|EG255599
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGC
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGC
EST: gi|76909942|gb|DV163615.1|DV163615
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|60339446|gb|DN206419.1|DN206419
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|22819171|gb|BU499261.1|BU499261
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|60336856|gb|DN203829.1|DN203829
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|7145412|gb|AW506893.1|AW506893
EST:     ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTGCGGGCGCCGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA
EST: gi|149108728|gb|EE189804.2|EE189804
EST:     ACCTTGCTTCCGGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGTTCTGTT                         CTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCGGAATGCA
genomic: ACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtattt ... ttctattcagCTTGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCTgtgagtatttttttttactttgtttatttagattagagtcagctttgatgcttatagtttgaggggaatagacaatggaacgcgacagactaaggtcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT