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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacagtaaaatcattttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

Basic information

species Zea mays
transcript GRMZM2G366935_T07
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
ttgacagtaaaatcatt-ttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
 ||    |||||   || | ||||||  ||||| ||||||  |  ||||||   |||||  || |||   ||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
-tgcttataaaacagttgtcgttctttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 4
ttgacagtaaaatcattttgttcttcactcatgaaggttcc-ctcatatggtcccaaattta--aaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
   | |||  | |  ||||  | |     ||||  ||||    ||||    |    || | |  | | | | |   ||||||| || |  ||| | || |||||| |||||||||||||| |||||||| | |||||||||||||||||||| |||| | || ||||||||||| ||||| ||||| |||||||| || || |
--tatagtgga-ttgtttttatatatgtccatgtgggttttattcatggatttgataactaagcagaaacattcctttcaatgcattttaatggtgttatcagGTCTTTGAGAAGCTTGGACCAAGCTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTCCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
--ttgacagtaaaatcattttgttc-ttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttat-tcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
  |  | |||    |  | | |||  || |||||||  | ||   ||  |  ||    || | ||   |  |||  | | |||| |     ||| |  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
cgtgtatagtgt--ttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 5
ttgacagtaaaatcattttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaat----atactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
       ||   | | ||  ||  || |   || |  |||  ||||| |     ||| |||| ||    ||  |   || |||| |  |  ||| | ||  ||||| |||||||||||||| ||||| || | |||||||||||||||||||| |||| | || || |||||||| ||||| ||||| |||||||| || || |
--tgtgatagtttgaattaatttctc-cctgtggac-ttcattcataagactggaaacttaacattgaaatcttcctttgaatgcactttaatggtgttaccagGTGTTTGAGAAGCTTGGACCAAGTTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTTCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

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|211042609|gb|FL405101.1|FL405101
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|93015243|gb|EB640763.1|EB640763
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|211070907|gb|FL383766.1|FL383766
EST:     CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGCGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|148983054|gb|EE028963.2|EE028963
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|21331443|gb|BQ486824.1|BQ486824
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|71439614|gb|DR820664.1|DR820664
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|60345840|gb|DN212813.1|DN212813
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|149000442|gb|EE037616.2|EE037616
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|211340986|gb|FL379602.1|FL379602
EST:     CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
                                              ttttgtc  CT-rich tract
         aaatttaaaatatact  TA-rich tract