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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA

Basic information

species Zea mays
transcript GRMZM2G093316_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattat------attgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
        ||||||           | | | | ||   ||  ||   ||| ||  || | || ||| |  ||| | | ||  | | |||      ||| |||||||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| || ||||||||||  || || ||||
-----ccacattctgcag-aattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G24970.1 (Glycine max), 3'ss of exon 5
tagaattgcattcttttttggacggaagga-gtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
|| | ||    |  |  |    |   |  |  |    |  |  ||| |   ||   ||||  |  || |   |  | |   |   || ||     |||||||| |  || |||||||||||||| |||||||||||| |||| || || ||| |||| ||||| ||||| ||||| || ||||||||||  || ||||| |
tacattttttcttgtcatcactcatcataatattagaaacttgtttacagtatttttcttcagtctacttatagaa-actgctgaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 6
tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatctt-gtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
|     ||     || | ||     |  ||      | ||  |   |   ||   | || ||| ||  |  | | |    ||   ||         ||||||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||| ||||| || ||||||||||  |  ||||| |
tgtttctggtggtttatctgataacatagaagtgggaatttctcgacagtatttgtttttgtggttcctt-atagaggcttctgaatcgccccttgaacagGTTGATGACAAGCTTTACATATACCTTGAATATGTATCTGGAGGCTCCATACATAAACTTCTTCAAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
tagaattgcattcttttttgg-acggaaggagtacatagttatttttcct-catgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
  |  || |||| ||  |||  |       | || ||| || |||    |   ||  | ||  |  || ||  |  | |   ||| || ||     |||||||| |  || |||||||||||||| |||||||||||| |||| || || ||| |||| ||||| ||||| ||||| || ||||||||||  || ||||| |
-tggtttacatttttacttgtcatcattatattagatacttgtttacagtatttgtcttttcagtctactcatagaa-actgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
tagaattgcattcttttttggacggaaggagtacatagttatttttcctcatgcatc-ttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
|     ||     || | ||     |  ||      | ||  |   |   ||   |  ||||| ||  |  | | |    || | || |       ||||||| ||| | ||||||||||||||||| |||||||| ||||| || || |||||||| ||||| | ||| ||||| || ||||||||||  |  ||||| |
tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttcctt-atagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
----------tagaattgcatt---cttttttggacggaaggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
           |||  |   ||   | ||| ||  |      | ||   |  | |||   ||||  ||  |  ||   ||    |     | | | |         ||  ||||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||  |||| ||||| ||||||||||| || ||||||||  | |||||||| |
gtaagttttacagatatttcttggacatttctgttctctgatactat-caactgtttcagctcaaccaagtcatgcacatgactagattctttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 3
tagaattgcattcttttttggacggaa--ggagtacatagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
     ||| | | |  | || |    |    | || ||   ||  |  |    ||  ||||  | ||||  |||||    ||      |||      ||||||| ||||| || || ||||||||   ||| ||||| | |||||| || ||| |||| ||||| ||||||||||| ||||||||||||   || ||||  |
-tcctttgaagtttcatctgcattacattatattagatcactagatggcgat-tgattcttcagcttatgtgaaattttccttggctatattccttgaacagGTGGATGACAAACTCTACATATATTCGGAATATGTATATGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGTTTGGTGAAATAGCTATTCATA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 6
-----tagaattgcattcttttttggacggaaggagtaca-tagttatttttcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
     |  |  | ||| ||   ||  |    |  || ||| ||| |     |     ||  ||||  | ||||  |||||    ||      |||      ||||||| ||||| || || ||||||||  |||| ||||| |||||||| || ||| |||| ||||| ||||||||||| ||| ||||||||   || ||||| |
tcctttgaagcttcat-ctgcattacattatattagaacactagatggcgat-----tgattcttcagcttatgtgaaattttccttggctatattccttgaacagGTGGATGACAAACTCTACATATATTTGGAATATGTATCTGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGCTTGGTGAAATAGCTATTCGTA

upper sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S44_113V6.1 (Physcomitrella patens), 3'ss of exon 4
---------tagaattgcattcttttttggacggaa---ggagtacatagttatttttcctcatgcatcttgtgattat----tcgaaatac----atctccatattatattgaaa-------acagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
          |   ||     | ||||   |   ||   |  ||   |      ||  |  |||   ||||||   | |    |||| ||      ||||   |      |||  |        ||| | || |||| | | || |||||  |||||||||||||||| ||||| || ||||| || ||||||||||||||    ||    || |  |   | ||||
gtgcgacgcaaaccttatgcaccttttaatatttaacatgacgtctgtcacatgttaactccattattcttgttgctttggggtcgacatgtcgggatctgactgcgtcgttgggatcttctggcagTTGGAAGATAGGTTGTATATATATTTGGAGTATGTTTCTGGAGGATCAATCCATAAACTGCTCCAAGAGTATGGCGCTTTCAAAGAGCCAGTGGTGCGCA

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|211515221|gb|FL355394.1|FL355394
EST:     TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACT                         GTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGG
genomic: TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACTgtatgtactg ... ttgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcatgcatcttgtgattattcgaaatacatctccatattatattgaaaacagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGTCAGTTTGGTGAACAGGCCATTCGCA
                                     atattatattgaaaac  TA-rich tract