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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 5
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                   || |||    ||| ||| |  ||    || | |    |||    ||   ||    |  |   |||||   ||| |  ||| | | |   |  ||  | || |  | ||| | || ||||| ||||| ||||| ||  | ||||||||||||||||||||||| || |||||||||||||||||||| || ||||||||||| || |||
-------------------aaatcatgtgatttttgtattga--ttatctcttatgattaccaaggccca----actctgaagcctaagcaa-tatatttatttttcttaactattgtttgtgt-agAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGTGATAATGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
gtattatttgtcctagctgaattca-acctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                 ||| |||| ||  |||  | |  ||   | |||    ||| || | | ||||  |||   | || |  ||  |  | ||  || |    |      |||  |||    |||  | || ||||| ||||| |||||||| || || |||||||||||||||||||| || || || |||||||| |||||||||||||||| |||||| |||
-----------------tgacttcatactaatttcttcttggt--ctatg-acatgatttatagtgtatt-tgttt-ctcacattctagttgactg--tttatataatggtgatgcacttg----tagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 5
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgct-tttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                    | |||    ||| ||| |  ||    || | |    |||  | ||   ||    |  |   |||||   ||| |  ||| | | |   |  ||  | |||  ||  ||| | || ||||| ||||| ||||| ||  | ||||| |||||||||||||||||||| |||||||||||||||||||| || ||||||||||| || |||
-------------------taatcatgtgatttttgtattga--ttatctcttatgattactaaggccca----actctgaagcctaagcaa-tatatttatttttcttaactattgtttatga--agAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGAGATAATGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 5
gtattatttgtcctagctgaat-tcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
             |  ||  || | ||  | || |||     |   ||||  |   | |   |   | ||    |  |  || | ||||| | |||     |  || |     |||  |||     ||| | || ||||| ||||| |||||||| || || |||||||||||||||||||| || || || |||||||| |||||||||||||||| ||||||||||
-------------tgacttcatattaatttcttcttg-gtctatgacatgatttatagtgtatttatttctcacattctaattgactttttatatg-----atggtga-----tgcacttg----cagATCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATATTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                 ||| |||  | |||  || |   |         |||   ||||   ||| || | ||||   |     || |       |  |  |     || ||  | ||  |   ||| | || ||||| ||||||||||| ||  | ||||| || ||||| |||||||| ||||| ||||||||||| ||||| || ||||||||||| ||||||
---------------attgatttcctcttatatttacgaag---------gtccagattc---agtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                ||  ||||    |  | |   |    | || |   |   | ||||    | |  |||| |   ||   ||||| |  | ||   | | ||  |       | |     |||  | |||||||| || || |||||  |  | ||  | || ||||||||||||||||| |||||||| || |||||||| || ||||| || ||  | || 
---------------tctttattctttttcgt-tcatataagagccttccatggtagttct---atgtt-tgtacatgtat---ctttttattttgacacaatttatgttataatatct----ctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------gtattatttgtcctagctgaattcaacctatt-attgcagggaaaccatgtgtctgaa--ttcttgagtatcatgtaaaccca-tagccttttcaaatggattaactgtaaatctc----tgcttttgggattagAG-CTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                                                    ||||    |    || |  |    |   || | | | ||| |  |    ||   || |  | | ||  | |   || | |  | ||   || |   |    ||   | ||  |       ||| ||  | ||||  | | ||| |||||||||| |||| ||| || ||| ||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| ||||| |||
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctga-attcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                                     || ||  | |  | |   |||| ||  | | | |  ||  |  |      ||  | |  ||| || | | ||   | ||  |     |||   | |||  ||| |  |      ||| |    | ||  | ||  |||||||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| |||||||| || |||||||| || ||  ||
gtaagaacgttttgcataaacctaatgcagcatgttttaatacctttgatgggctaatttaatgt-tcaatatagaaatgcatatcatccaataggcttaaggaacttgatgatcc-catttacttcctcttgat--actatttactgtgtcttctattttaagGACGGAGCTGGTGCCTGCATATGTGCGCCTACTTCGTGATAATGAAGCTGAAGTACGCATAGCAGCTGCCGGAAAAGTTACAAAGTTTTGTCGGATTCTA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 6
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
             |   || |||     ||||  ||       | | ||||||    || |     || || || |   || |   |||   |   || |    ||| | | || | ||  |   ||  | || ||||| ||||| ||||||||  | |||||||| |||||||||||||| || ||||||||||| ||||||||||| || |||||||| || || 
-------------tttttggatt-ggtttattcctg-------atc-tgtgtccattttttaacaaattatttatata-attgttattt--gacttatgattgataattatttgatattttg--cagGTCAGACTTGGTTCCTGCATATGTTCGGTTGCTTCGTGACAATGAGGCTGAAGTACGCATAGCAGCTGCAGGAAAAGTAACAAAATTTTGCCGGATTTTG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                 | |  ||||  | |  | ||         || |   ||| ||| |   | || |     |        ||||    |   ||   |     |  ||| | |     | ||| | || ||||| || || ||| | ||  | ||||| ||||||||||||||||| || |||||||||||||| ||||||||||| || || |  || |||
-----------------taatctcaagttttcctggc-------ttatct---tgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA

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|32831601|gb|CD971279.1|CD971279
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|33091965|gb|CF051959.1|CF051959
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|22935744|gb|BU572019.1|BU572019
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|32851452|gb|CD991133.1|CD991133
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG                         AGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA
genomic: GCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
                       gattaac  putative branch site (score: 2)
                                    tctctgctttt  putative PPT
             ttttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA