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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctgttgatgttcttgccacatgctaaatcttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca...

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 7
ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatt----tgc-tgttgatgttc-ttgccacatgctaaatcttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca
 | | |||   |||||| || |||||||| |||||  | ||||||||||||||||||||||||||||| |||||||||||    ||| ||||||  ||| ||||    |  ||  ||| ||   |        |      || |    | || | |  |    ||  | |   ||      
GTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAGgtattattttgcctgttgaacttcattgctctcttttatgtctactgccatcagaggatgagagttttaccaagcagttctctgattttgtctgtcgctg------

upper sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g26870.1 (Oryza sativa), 5'ss of exon 7
------------------ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatt----tgc-tgttgatgttc-ttgccacatgctaaatcttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca
                   | | |||   |||||| || |||||||| |||||  | ||||||||||||||||||||||||||||| |||||||||||    ||| ||||||  ||| ||||    |  ||  ||| ||   |        |      || |    | || | |  |    ||  | |   ||      
AAACTGCCTATACTGCAGGTAGGTGACCATACAGAAAGTATCACCTTTGATCTAAGACCTTCAGATGCCATAAACATTGCTGTTCGCTGCAAGgtattattttgcctgttgaacttcattgctctcttttatgtctactgccatcagaggatgagagttttaccaagcagttctctgattttgtctgtcgctg------

upper sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 6
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 5'ss of exon 8
ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgta---tttgctgttgatgt---tcttgccacatgctaaat-cttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca
 | | | ||   | ||| ||| |||  || || ||||| |||||||||||||| |||||||||||| | |||||||||   ||   ||| | |||   |  ||  || |  || || ||| ||||         | | || | || ||   |   | ||     |  |||| |||       
GTGGGTAATGAAAAAGAGAGCGTCAGTTTTGACCTTCGACCTTCAGATGCCATTAACATTGCTGTTAGATGCAAGgtactcttcattgtgggtgtgagttgtgtgactttatacatgcttttatttggtcacagtatcttttgcagatgccaatctgtaactagtttttatctgt-------

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|33100890|gb|CF060850.1|CF060850
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTACTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|14244855|gb|BG842793.2|BG842793
EST:     CCTTCGATCTCCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13562234|gb|BG550454.1|BG550454
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTGCAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|16925921|gb|BM078989.1|BM078989
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|5895762|gb|AW037008.1|AW037008
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTT
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTT
EST: gi|14243138|gb|BG840841.2|BG840841
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|60353604|gb|DN220577.1|DN220577
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13178078|gb|BG349336.1|BG349336
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|211186706|gb|FL252851.1|FL252851
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|60346391|gb|DN213364.1|DN213364
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|89755425|gb|DY685846.1|DY685846
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|60355084|gb|DN222057.1|DN222057
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|33100633|gb|CF060593.1|CF060593
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGGCCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|211436290|gb|FL481825.1|FL481825
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|28984501|gb|BQ539125.2|BQ539125
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|33102029|gb|CF061989.1|CF061989
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGGCCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13178561|gb|BG349819.1|BG349819
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13177698|gb|BG349129.1|BG349129
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|211507463|gb|FL431647.1|FL431647
EST:     CGATCTTCGGCCTTTCAGATGCCATAAACATTGCTGTTTGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CGATCTTCGGCC-TTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|78113266|gb|DV531659.1|DV531659
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTANCA-GTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACC
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTA-CAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACC
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13249994|gb|BG360897.1|BG360897
EST:     ATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: ATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|16377885|gb|BI992166.1|BI992166
EST:     TGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: TGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGATTCTACAGACAGCATCACCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctgttgatgttcttgccacatgctaaatcttctattactctgatttttattattcatattgaaggttttagtgcatgcttatttgtgggagca

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