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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcgtcgctcgaatcccatcccattgccatccgacgaggagaagacaccacctgtgactgacggatcgactcaactgaactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACGTCGTGCGGCGACAAGGATGTGTGCCACCCGACGGACGCGCAGGCGGCGG

Basic information

species Zea mays
transcript GRMZM2G020484_T08
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020484_T08 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g04950.1 (Oryza sativa), 3'ss of exon 3
gtaagatcgtcgctcgaatcccatcccattgccatccgacgaggagaagacaccacctgtgactgacggatcgactcaactgaactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACGTCGTGCGGCGACAAGGATGTGTGCCACCCGACGGACGCGCAGGCGGCGG------
        ||  ||  ||||   |   ||| |  |        |  | ||       |||||  || |       |    |||      |||||  ||||| ||||||| ||||| |||||||||||||||||||||||  |||      |||||   |  | ||| ||||||||||| |||||| ||| ||      
--------gtaact--aatcgtcttggatttcagtttctgattgctatgatcgatggtgtgatcgaagagagagatgttttgatggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCGT------GCGACGGAGGAGCGTGTCACCCGACGGAGGCGCAGACGGGGGTGGTGT
















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|211365735|gb|FL263996.1|FL263996
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|148974530|gb|EE025317.2|EE025317
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|149099731|gb|EE185781.2|EE185781
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|89760037|gb|DY688639.1|DY688639
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|148972810|gb|EE023795.2|EE023795
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCCTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|78112564|gb|DV530958.1|DV530958
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGCCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|74234545|gb|DT642459.1|DT642459
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|76936415|gb|DV174717.1|DV174717
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|149101742|gb|EE287361.2|EE287361
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|101394497|gb|EB819183.1|EB819183
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|149074406|gb|EE162795.2|EE162795
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|211049421|gb|FL097868.1|FL097868
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|50323834|gb|CO518960.1|CO518960
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCCTCGGTGAAGGG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGG
EST: gi|71439086|gb|DR820136.1|DR820136
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|76925417|gb|DV170443.1|DV170443
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
EST: gi|148949850|gb|EC895341.2|EC895341
EST:     ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTC                         GGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG
genomic: ACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaagatcgt ... aactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgaggagaagacaccacctgtgactgacggatcgactcaactgaactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACGTCGTGCGGCGACAAGGATGTGTGCCACCCGACGGACGCGCAGGCGGCGG
                       gactgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcgtcgctcgaatcccatcccattgccatccgacgaggagaagacaccacctgtgactgacggatcgactcaactgaactgaacagGGCCTGGCGCTGCTGACGATGGCTTCGTCGGTGAAGGGGCTGGTGCCTACGTCGTGCGGCGACAAGGATGTGTGCCACCCGACGGACGCGCAGGCGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG