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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag

Basic information

species Zea mays
transcript GRMZM2G107696_T02
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 5'ss of exon 16
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgcca-ctgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag
|| ||||| || |||||||| ||||||||||||||||  ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||||   | | | | | |   | ||   | | |   |  || || ||||||||  ||   ||  |  |||  ||  |  || |  |||  |  |     |||    |  |   || ||  || |||
GGGTTCAATTATCTTCATTGCCAGAAAGCTGCTATTAGTACATCAAACACAGGAGTTGAGGAGGCGATGAATTGGCTTCTCTCACACATGGATGATCCAGgtcagtatacaaacagaaatgttacatattact-tctttgtcatcatgaaaggatgattggccgtcttgtaatttgtaact--tgaccgctacaaacttta---atcacctttctgctatacag

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA06G39770.1 (Glycine max), 5'ss of exon 16
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag
||||| ||| | || |||||||||||||||||||| || ||||||||    ||||| || || || ||||||||| |  | || ||||||||||||||||||  |  || || |  | |||| | |  || |       | ||    |  ||   | |        ||||    | || |  ||  | | | ||||||| | ||                   
GGCTTTAACCATCTCCATTGTCAGAAAGCTGCTATAAATACATCAAATGTTGGAGTAGAAGAGGCAATGAATTGGTTGTTATCTCACATGGATGATCCAGgt--acctgtcatt--ttttttatgtaaaaca-------tatttgaaagttacctggtaa------tccaggacataa-tgctgt-ataaatttgttttacgtag------------------

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA12G22240.1 (Glycine max), 5'ss of exon 16
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctctt-ttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag
||||| ||| | || |||||||||||||||||||| || ||||| ||    ||||| || || || ||||||||| | || || ||||||||||||||||||  |  || || |  | |   | |  |  | ||  |  || ||  | |  ||   |    | ||  ||||    || |||  || || | | ||||||| | ||                   
GGCTTTAACCATCTCCATTGTCAGAAAGCTGCTATAAATACATCCAATGTTGGAGTAGAAGAGGCAATGAATTGGTTGCTATCTCACATGGATGATCCAGgt--acctgacatttttttaactatcatgtaaaacaaacttgtttgtaagttacctg----gtaatatccaggacaataatgctg-gataaatttgttttacgtag------------------

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: Vv03s0017g00950.t01 (Vitis vinifera), 5'ss of exon 2
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagaga---gaattgttttccataaaattattttg-tgatgcag----------------------
|| || ||| | |||||||| |||||||||||||||||||| || ||  | ||||| || || |||||||||||| | || || ||||||||||||||||||  |||    |     |  | |   |  ||| |   |||           |||   |  | | || |       || ||  |||   |   ||  |||||    || | | |      |||| | |                      
GGATTTAACCATCTTCATTGCCAGAAAGCTGCTATTAACACGTCTAATGCTGGAGTGGAAGAGGCGATGAATTGGTTGCTATCACACATGGATGATCCAGgt--attgcaaatcaaacagtcgcaatagatatttgctttagcagaaggcaaatacttaggaagctcctgcctccaagattgtgaataacttgatgtgtttatggtagactgaggggaatgataccgatgggcatttttttttttccag

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: Vv19s0014g03910.t01 (Vitis vinifera), 5'ss of exon 4
-GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag
 || || ||| | |||||||| |||||||||||||||||||| || ||  | ||||| || || ||||| |||||| | || || ||||||||||||||||||  ||     |     |  | |      ||| |   |||   ||  |   ||    |  | ||  ||| |  |  ||  |||| ||   | ||| | |   ||                   
GGGATTTAACCATCTTCATTGCCAGAAAGCTGCTATTAACACGTCTAATGCTGGAGTGGAAGAGGCGAT-AATTGGTTGCTATCACACATGGATGATCCAGgt--atcgcaaatcaaacagtcgcaacagatatttgctttag-cagaaggcaaatacttagaaagctcctacctcgaag-attgtgaataacttgatgtgttta-------------------

upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 20
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 5'ss of exon 17
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagaga---gaattgttttccataaaattattttg-tgatgcag-----------------------
|| || ||| | |||||||| |||||||||||||||||||| || ||  | ||||| || || |||||||||||| | || || ||||||||||||||||||  |||    |     |  |||      ||| |   |||           |||   |  | | ||         || ||  |||   |   || ||||||    || | | |      |||| | |                       
GGATTTAACCATCTTCATTGCCAGAAAGCTGCTATTAACACGTCTAATGCTGGAGTGGAAGAGGCGATGAATTGGTTGCTATCACACATGGATGATCCAGgt--attgcaaatcaaacagttgcaacagatatttgctttagcagaaggcaaatacttaggaagctcgtgcctcgaagattgtgaataacttgatttgtttatggtagactgaggggaatgatactgacggacactttttttttttccag

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|116817395|gb|EC860237.1|EC860237
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAATGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|211494928|gb|FL217185.1|FL217185
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAATGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|116819768|gb|EC862916.1|EC862916
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAATGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|31361116|gb|CD445473.1|CD445473
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|149014867|gb|EE044578.2|EE044578
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|60345352|gb|DN212325.1|DN212325
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|60339263|gb|DN206236.1|DN206236
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|101383461|gb|EB813786.1|EB813786
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|71595705|gb|DR906456.1|DR906456
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|60350109|gb|DN217082.1|DN217082
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|50331230|gb|CO526356.1|CO526356
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
EST: gi|71330489|gb|DR802011.1|DR802011
EST:     AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAG                         ATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG
genomic: AGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgc ... tgtgatgcagATATAAACGACCCAATATCAAAAGATTCACGTGCTTATGAGCCATCTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTCAACTACCTTCATTGTCAGAAAGCTGCTATTAACACATCAAACACAGGAGTTGAGGAAGCGATGAATTGGCTCCTCTCGCACATGGATGATCCAGgttgatttgccactgctcttttgtttttaataatgattttcttcatgaaataatcgatgtgcaacttccaaagtaaaaatattgagagagaattgttttccataaaattattttgtgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA