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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_T01
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|78087348|gb|DV515741.1|DV515741
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211026991|gb|FL377493.1|FL377493
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTKCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|89755821|gb|DY686098.1|DY686098
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211199112|gb|FL383376.1|FL383376
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|89252932|gb|DY624718.1|DY624718
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211284822|gb|FL429278.1|FL429278
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211284823|gb|FL429279.1|FL429279
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211323238|gb|FL374213.1|FL374213
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211539558|gb|FL409998.1|FL409998
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACGGGGCCAG-CACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211228051|gb|FL407860.1|FL407860
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATSGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211355536|gb|FL044624.1|FL044624
EST:     GCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACT
genomic: GCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGA-Ggtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACT
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     TTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: TTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|93016182|gb|EB641702.1|EB641702
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|211063859|gb|FL423538.1|FL423538
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: GGCCGCCGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... ctgcgcgcagCGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAG                         CGGCGGTGGCGTGGGGACCGGGCCAGCCACTGGTGATGGAGGAGGTGGAGG
genomic: CGCCGATGCATCTTCGTTGCCTCCGTCCGCCATCACCTGCCGAGgtattagccc ... 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