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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaatctagttgactgatctgtaagaacaaactaatgcattttcagtgggtagaccattgacattaataaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 6
gtaccaatctagttgactgatctgtaagaacaaact-aatgcattttcagtgggtagaccattgacattaa------taaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
||||  ||  ||   | |  | |  || |  ||||| ||  ||  || |||| ||| |  | |  ||||||      |||| |||||||  ||   ||||||| | | |||   |||||| || |||||||| |||||  | ||||||||||||||||||||||||||||| ||||||
gtacttatgcagagcatt--ttttaaaaaggaaactgaactcaactttagtgtgtacaatactatcattaaccattttaaactagaaactgcctatactgcagGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAG

upper sequence: GRMZM2G006468_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 7
----gtaccaatctagttgactgatctgtaag-aacaaactaatgcattttcagtgggta--gaccattgacattaataaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
     | ||            || ||| |||   |    ||  | | |  | || || ||  |   ||  |     || | || | |      |    ||||| | | | ||   | ||| ||| |||  || || ||||| |||||||||||||| |||||||||||| | ||||||
gcatattcctgctgtaccccttgttctttaattgattgccttgtacttcattagaggatacaggtgatcaattgacatgatgttgga-----tgtggatgcagGTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAG
















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|60399773|gb|DN232583.1|DN232583
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGC
EST: gi|33100890|gb|CF060850.1|CF060850
EST:     GTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAG--A-CATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: GTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|14244855|gb|BG842793.2|BG842793
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTCCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|16925921|gb|BM078989.1|BM078989
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|5895762|gb|AW037008.1|AW037008
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|14243138|gb|BG840841.2|BG840841
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60353604|gb|DN220577.1|DN220577
EST:     AAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: AAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|13178078|gb|BG349336.1|BG349336
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|211186706|gb|FL252851.1|FL252851
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60346391|gb|DN213364.1|DN213364
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTTTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|89755425|gb|DY685846.1|DY685846
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|76010926|gb|DT938096.1|DT938096
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60355084|gb|DN222057.1|DN222057
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|33100633|gb|CF060593.1|CF060593
EST:     ACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: ACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|211436290|gb|FL481825.1|FL481825
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|28984501|gb|BQ539125.2|BQ539125
EST:     CAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: CAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|33102029|gb|CF061989.1|CF061989
EST:     ACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: ACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|13178561|gb|BG349819.1|BG349819
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|13177698|gb|BG349129.1|BG349129
EST:     T-AGCAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|71774337|gb|DR972215.1|DR972215
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTAC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTAC
EST: gi|78113266|gb|DV531659.1|DV531659
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG                         ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC
genomic: TAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAGgtaccaatct ... ggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcagtgggtagaccattgacattaataaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG
                       cattaat  putative branch site (score: 3)
                        attaataaagtagaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaatctagttgactgatctgtaagaacaaactaatgcattttcagtgggtagaccattgacattaataaagtagaaacatccggcactgcagATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT