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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttttttgctcttgatctttttgtttttgtgttaatgtacatctgacactatgtatttggtaaaggtaccaattaaatcctccagtttcacaag...

Basic information

species Zea mays
transcript GRMZM2G035150_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 7
GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttttttgctcttgatctttttgtttttgtgttaatgtacatctgacactatgtatt-tggtaaaggtaccaattaaatcctccagtttcacaag
||  || || ||||||||||||||||||||||||||||||||||||||||||||  |  | |   |    |   |   || ||   | | | | | ||||    |  | ||| || |  |   |  ||| | |       || |   |  
GAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaagatgatgtttccacacttcctgacttattaaataattattcttctgtttatcggaattatgctgtatacag-aataagagttatttgtattggaca

upper sequence: GRMZM2G035150_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G35300.3 (Glycine max), 5'ss of exon 8
GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttttttgctcttgatctttttgtttttgtgtta-atgtacatctgacactatgtatttggtaaaggtaccaattaaatcctccagtttcacaag
 ||||| ||||||||||| || || |||||||||||||||||||| | ||||        |      |  || || | |||||   ||  || ||   ||    || | |  ||||  | | | |  | |   |   | | | | |    
AAGTGGCGAATGGGGTGATCATGTCACATTGCAGGCTGCTGCAGATTGGgtatgaggaaataaacagttttcattctattttttccttgtatataatacttttccttttttattggctatgttgcttagtgcctttgcaaatgtaattg-

upper sequence: GRMZM2G035150_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G32220.1 (Glycine max), 5'ss of exon 8
GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgta----aactttttttgctcttgatctttttgtt-tttgtgttaatgtacatctgaca-ctatgtatt-tggtaaaggtaccaattaaatcctccagtttcacaag
|||||| ||||||||||| || || || ||||||||||||||||| | ||||     |  |   | | | |   ||| | | ||   | |  |  | |   | |     |||||| |  | ||     | | |||  |||  |    ||||     
GAGTGGCGAATGGGGTGATCATGTCACGTTGCAGGCTGCTGCAGATTGGgtatgaggaaataaatgggtttcattctatattttgcctatacttttctttttttattggctatgtttcctagtgcctttgcaaatgtaat--tgagatttc-----

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|74235678|gb|DT643592.1|DT643592
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|4804174|gb|AI666040.1|AI666040
EST:     GTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|166563741|gb|EG244809.1|EG244809
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCC
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCC
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG                         TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT
genomic: GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttt ... gcttttgcagTACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGgtaaactttttttgctcttgatctttttgtttttgtgttaatgtacatctgacactatgtatttggtaaaggtaccaattaaatcctccagtttcacaag

 AGTGGA
- GTGGAG
-  TGGAGA
- - GGAGAA
- - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - CTGCAG