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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagcccgccccgccttgcttcttgcgtagggtttagtggcgagtaaaattggatggcctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTC

Basic information

species Zea mays
transcript GRMZM2G149272_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 1
--------------------------gtattagcccgccccgccttgct-tcttgcgtagggtttagtggcgagtaaaat-tggatggcctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTC
                          ||     || || |||    |   | ||| |  ||   |  ||| |  |   || ||  ||   |||| |||||||||||||||||||  || || ||| | ||||||||||||||||||||||| || ||||||| | ||||||||||||| ||||||||||||||||||||
gtacgtacgagccccccctcggccgagttactccctgctccgttgcgtggttttgtggtggtgattttggtggatgggatatgcctgcgttgcgtgcagCGGCGGTGGCGTGGGCGCCCGGTCAGGCGCTGGTGATGGAGGAGGTGGAGGTGGCGCCGCCGGAGGCCATGGAGATCCGCGTCAAGGTCGTCTCCACCTC
















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|211521058|gb|FL044641.1|FL044641
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211521056|gb|FL044639.1|FL044639
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211353144|gb|FL044621.1|FL044621
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355542|gb|FL044630.1|FL044630
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211521054|gb|FL044637.1|FL044637
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211353142|gb|FL044619.1|FL044619
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355543|gb|FL044631.1|FL044631
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211521055|gb|FL044638.1|FL044638
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211353139|gb|FL044616.1|FL044616
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355544|gb|FL044632.1|FL044632
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355540|gb|FL044628.1|FL044628
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211353143|gb|FL044620.1|FL044620
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGACCGCCATCACCTGCCGAG                         CGGCGGAGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355546|gb|FL044634.1|FL044634
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211521057|gb|FL044640.1|FL044640
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355545|gb|FL044633.1|FL044633
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355536|gb|FL044624.1|FL044624
EST:     GCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACT
genomic: GCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGA-Ggtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACT
EST: gi|211355535|gb|FL044623.1|FL044623
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgcttcttgcgtagggtttagtggcgagtaaaattggatggcctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTC
                             agtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagcccgccccgccttgcttcttgcgtagggtttagtggcgagtaaaattggatggcctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGGTCGCCCCGCCGGGGCCCATGGAGATCCGTGTCAAGGTCGTCTCCACCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC