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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

Basic information

species Zea mays
transcript GRMZM2G121942_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 3'ss of exon 2
-------ggttcaactggatcttag-tcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaattta-ctatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
        ||| || |   |  ||  | |||| ||  | ||  |||      |  | |   ||||| |     ||  || ||  | || | | ||  || |||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | ||||
tttattcagtttaaatatgttgtaccttttcaatgaac-tttggtaat---atccttttgtattttgaccatgatgttgatatgataaatcatcttctttaaagGCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G40200.2 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------------ggttcaactggat----cttagtct-tcagtgttcgttcagt---agctag-gttttctgacattttcaa-tgcaatactgctaacacaatttac---tatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                                | ||||| |   |     | ||| | ||| | |  |  |  |   |  | | |||   |    ||||||| | |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
gtagagattctattcccaatttccttgaaacgctctttccctctttccgttcactcgctccgttatgaagttcaggctgcgattcaattttgtacttttcagtttctcaatctgtgacctatgtgaattggagttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------------------ggttcaactggatcttagtct-tcagtgttcgttcagt---agctag-gttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---aggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                                             ||    |   | | ||| | ||| | |  |  |  |   | || | |||   |    |||| ||      |     ||   |||||   | ||  |   ||||||| |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   |||||
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
-ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttac---tatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
    |   | |  ||| | |||      |  ||  | | |  || |  |  |   |||  ||| |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
gtacttttcagtttctcaatctgtgacctatgtgaattgg--agttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------------------------ggttcaa--ctggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---aggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                                         | | ||  ||||     | |       |||| |  |   | ||||||||    ||      |   | |  ||  | | || |||  | |||      |||| || |||||||| |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| ||||||   |||||
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagc----agatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 3'ss of exon 1
ggttcaactggatcttagtcttc---agtgttcgttcagtagctaggttttctgacattttcaatgcaata-ctgctaacacaa--tttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
   | |  | ||| |   ||||    ||  |   |  |  |  | ||           ||| |||  || | ||  |         |||  | |||   |||| || |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  ||||||
-aattaggtcgatttgtttcttataaagcatatatagatgaaatcgggaacaatttgctttaaatttaacatcttttggtttgggtttttttcttttgcagGCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
ggttcaactggatcttagtcttcagtgttcgttcagtagc--taggttttctgacattttcaat-gcaat--actgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
 ||         | ||  | ||     | | || | | |    | |   |    ||| || | | | |||  |     |     || |   |||  | |||| || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

upper sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ07968 (Selaginella moellendorffii), 3'ss of exon 1
ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT--------------
                     | |||   || ||  |  |    | |||  |  |  |||  |    | || || |   ||||  |       |||| |||||| | |||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || ||  |   | ||||              
--------------------gtaagtaagcgctcgatctc----tcttcccatttcctcagcg----attggtagc--gatttcttgc-----agGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA

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|211191926|gb|FL276014.1|FL276014
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191933|gb|FL276021.1|FL276021
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211191933|gb|FL276021.1|FL276021
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211191922|gb|FL276010.1|FL276010
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191923|gb|FL276011.1|FL276011
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211088952|gb|FL225885.1|FL225885
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211088952|gb|FL225885.1|FL225885
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|45847222|gb|CN071165.1|CN071165
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191929|gb|FL276017.1|FL276017
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|78111599|gb|DV529996.1|DV529996
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191928|gb|FL276016.1|FL276016
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|18163701|gb|BM333540.1|BM333540
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|101402755|gb|EB822903.1|EB822903
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191930|gb|FL276018.1|FL276018
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211191930|gb|FL276018.1|FL276018
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|149110102|gb|EE293919.2|EE293919
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211194322|gb|FL276024.1|FL276024
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211194322|gb|FL276024.1|FL276024
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|5108428|gb|AI740141.1|AI740141
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCTGA-CAAAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211194323|gb|FL276025.1|FL276025
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211194323|gb|FL276025.1|FL276025
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|32864255|gb|CF003937.1|CF003937
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCTGA-CAAAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|18171587|gb|BM341427.1|BM341427
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191925|gb|FL276013.1|FL276013
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211194325|gb|FL276027.1|FL276027
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211194325|gb|FL276027.1|FL276027
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|149076642|gb|EE165281.2|EE165281
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211194324|gb|FL276026.1|FL276026
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|211194324|gb|FL276026.1|FL276026
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         G
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctag-
EST: gi|32943241|gb|CF048060.1|CF048060
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCTGA-CAAAGCACACCATCATGCAG                         CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGT
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGT
EST: gi|211088951|gb|FL225884.1|FL225884
EST:     GTTGCCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: GTTG-CCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|60350040|gb|DN217013.1|DN217013
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211191934|gb|FL276022.1|FL276022
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGT
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... gaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGT
EST: gi|211191924|gb|FL276012.1|FL276012
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg
EST: gi|211194321|gb|FL276023.1|FL276023
EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGGCTAG                     
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCAT----GC-AGgtgggtagta ... gaaagg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgacattttcaatgcaatactgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                        tgctaac  putative branch site (score: 1)
                                 aatttactatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - -ctggatc
- - - - - - - - - - - - - - - - -cagtagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacaa