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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGATGCTGTTCTTCTAATAGCTGCTGTATTACCTGACCGCGATATCAAATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgagttgttcttgctatatactttatatgttgtttcaacagccacctcttgtttctcttgagtgttgagtcattttagtgatgcaactggactgtgttgctgaag

Basic information

species Zea mays
transcript GRMZM2G169516_T05
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169516_T05 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 6
TGCAGATGCTGTTCTTCTAATAGCTGCTGTATTACCTGACCGCGATATCAAATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgagttgttcttgctatatactttatatgttgtttcaacagccac-ctcttgtttctcttgagtgttgagtcatttta---gtgatgcaactgg------actgtgttgctgaag-----------------------------------------------------------------
 ||||||||||||||||| || |||||||| |||||||| |  |||||||| || ||||||||||| |||||||||||||| ||||||||||||||||||||| |||||||| ||  ||  ||||  |||| ||||     ||    | || ||||| | |    ||  | | |||||||| ||   ||| |||||||        | | | ||  |  |                                                                  
AGCAGATGCTGTTCTTCTGATTGCTGCTGTCTTACCTGATCTTGATATCAAGTATATGTTGAAAATATGCAAAATACTTGGCATGGCTGCTTTAGTTGAGgttagctgagttatttgtg--atatgttttacatgtcaaagcacttccaactctcttatgttagctgctt-tggagtcattctactagtgttgcaacttccaattcattttcttcttccaagtaaatcaaatgcaacctcaatattcaaattttgatttaataaacaagctaaatgtgttctgaag

upper sequence: GRMZM2G169516_T05 (Zea mays), 5'ss of exon 6
lower sequence: AT5G48220.3 (Arabidopsis thaliana), 5'ss of exon 7
TGCAGATGCTGTTCTTCTAATAGCTGCTGTATTACCTGACCGCGATATCAAATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgagttgttcttgctatatactttatatgttgtttcaacagccacctcttgtttctcttgagtgttgagtc-attttagtgat-gcaactggactgtgttgctgaag
 |||||||| ||| |  | || ||| |||| ||||||||||  || |||||||||||| | || ||||||||||||||||| |||||| |  | || |||||| | | |   |||     ||||  | | |  |  || ||   | | | | || |  | ||  | ||||||      |||||  || |  | ||| | || |          
CGCAGATGCAGTTTTGTTGATCGCTTCTGTGTTACCTGACCTTGACATCAAATACATGATTAAGATTTGCAAAATACTTGGAATGGCTACACTTGTGGAGgtttg-taaccagtttca--tatacgcctcaactaatgctt---ctgtctcttcctaatcctaattagtgtttttctgattttcttggttaccacttgcctctag--------
















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|71430054|gb|DR811104.1|DR811104
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGAGGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|71759609|gb|DR957546.1|DR957546
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|32928612|gb|CF033424.1|CF033424
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTA
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTA
EST: gi|166583653|gb|EG054917.1|EG054917
EST:     GGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGNGTTTTAGGGATTGATGGTGTACAG
genomic: GGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|71324170|gb|DR798788.1|DR798788
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|24934455|gb|CA452673.1|CA452673
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGT
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGT
EST: gi|211501402|gb|FL138828.1|FL138828
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|71433347|gb|DR814397.1|DR814397
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|71759019|gb|DR956956.1|DR956956
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|211073093|gb|FL464915.1|FL464915
EST:     CATG-TGAAAATTTGCAAAATACTGGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: CATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|94473827|gb|EB702785.1|EB702785
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|91870855|gb|EB401116.1|EB401116
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|24765189|gb|CA400348.1|CA400348
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|88752600|gb|DY536741.1|DY536741
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|6973599|gb|AW438335.1|AW438335
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
EST: gi|71431465|gb|DR812515.1|DR812515
EST:     AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAG                         GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG
genomic: AATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgag ... gttgctgaagGTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGATGCTGTTCTTCTAATAGCTGCTGTATTACCTGACCGCGATATCAAATACATGTTGAAAATTTGCAAAATACTTGGGATGGCTGCTTTAGTTGAGgttcgctgagttgttcttgctatatactttatatgttgtttcaacagccacctcttgtttctcttgagtgttgagtcattttagtgatgcaactggactgtgttgctgaag

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