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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag

Basic information

species Zea mays
transcript GRMZM2G110983_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag
|||||||||||||||| ||  |||||||||| ||||| || ||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || |||||||| | ||    |       |     ||||   | |||     |||   |||    |||  || | ||  |    ||||  |   | |||| |||
TGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAACAATATAATGCTTTGGAATGCTGTAATTTTTGGgtaaggtgttagacttaagagatatgttttattc-ctttcggttttattttgatccattatacttagttgtcaattatgtct---tgttttgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G10640.3 (Glycine max), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca--gaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag------
| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||  | || |  |||                 |    || ||||  ||||||  ||   ||  || | || |||   | |  || |||     ||        
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgctta-cttgaataatatagtt--actttgttttttattttattttttttccacactttgtgta

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaat--atttgacatcgtctttggatatgcttatttcttttacag-----------------------------------------------
||||||| || |||||| || ||   || ||||| || || || || || || ||||| |||||||||||||||||||||||||||||||||||||||||||  | ||   ||| |     |    |    || |  | ||  ||| | || || |  ||| | ||   | |||  || | ||||| |  ||||                                                  
TGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtgagttg---aattcaaattcgatataggtccaa--tgttgttttaatttatagtcaattggtcactattttttaat-ttcttatgttgtttaattactgatggataagtgatttttggtttcttgactgctttggattgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca--gaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag--------------------------------------------------------
| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||  | || |  |||                 |    || ||||  ||||||  ||   ||  || | || |||   | |  || |||     ||                                                          
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagctgaattgaaattggataaagataaaactgttctgctta-cttgaataatatagtt--actttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca--------gaatccccccgcccccttttccccacttcttagtttgaattgtaatatt-tgacatcgtctttggatatgcttatttcttttacag-------------------------------------------
| ||||| ||||||||| || ||   || ||||| || || || || || || || || |||||||||||||||||||||||||| ||||||||||||||||  | || |        | ||         |  || | |  ||||      |  | |  || |  | | |  |  | |||    |  |||  |     ||  |                                           
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATAACAACATAATGCTGTGGAACGCTGTCATATTTGGgtgagttgaattgaaattggataaagagaaactattctgcttacttgaataatatagtcatactgctattattttattttttcccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttct---tttacag
| ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||| |||||||| ||||| |||||||||||||||||||||||  |||   |      ||      |  |  | |  | ||  |   | || |   ||||     | |  || ||  |  || |||||   |||  ||
TAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAACAACATTATGCTCTGGAATGCTGTCATATTTGGgta--atgggaacaagtacctttagatactggctaaatatttctgaaacttttgtcatttctgtacttacttagacctttttgtttctaaatttgtag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgta-tgatgcagaatccccccgcccccttttccccacttcttagtttgaattgta--atatttgacatcgtctttggatatgcttatttcttttacag
||||||||||||||||| |||||  ||| ||||| || || || || ||||| || || || || ||||| || ||| ||||||||||||| ||||| ||||| |    |  ||    |            |   ||||  ||| ||    || |   || ||   |  |  | ||  | ||  | |           
TGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAGACAACAATATCATGTTGTGGAATGCTGTTATATTCGGgtaattgaactaaagtaacaaaaaaaaaaaacgatacttgataggtttctctgcactgtacttattaaagcttctgattgtggatttgcag-------

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcaga----atccccccgcccccttttccccacttcttagtttgaattg----taatatttgacatcgtctttggatatgcttatttcttttacag---------------------------
||||||||||||||||| || |   ||| || ||||| || || || ||||| || || || || ||||| ||||||||||||||||| || ||||||||||| | ||   |    || | ||  |    |    |  |  |||  |||| | | |    | |||| ||   |  |   | || |  |||||||   ||  |                            
TGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACAACAATATAATGCTGTGGAATGCAGTTATATTTGGgtacgttgggaatgatatgctccatcattttaaatctaatctctgtgtttcattagagttttatatctgtatttatgcatagagagacttatttaagtttaacttattcaattcttggttttcactgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 2
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcag---aatccccccgcccccttttccccacttcttagtttgaattgtaat--atttgacatcgtctttg--gatatgcttatttcttttacag--------------------------------------
||||||| ||||| ||| |||||   |||||||| || |||||||| ||||| || || || || ||||| |||||||| ||||||||||| |||||||||||    |||    ||| |       |  || |      | ||||  ||   |  | ||  ||||| | |   ||||     |||| |||  | |  |                                          
TGATGAGAGATTTTAAGAGGTTGCAACAGGACCCCCCTGCCGGCATCAGTGGAGCTCCCCAAGACAACAATATAATGCTTTGGAATGCTGTTATATTTGGgtaatgggcaacaaaattcatgaaaactgttattgtgtttgcttatgttatgtgtttatttatttgccttttactttctcagtatgtttaagtatggttggataagccatttctggtttcttttctgatttggattgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 5'ss of exon 3
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttct-tagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag------------
| ||||||||||||||| |||||   ||||| || || || ||||| ||||| || || || || || ||||| ||||| ||||||||||| ||||||||||||| ||   ||| |  |        ||    |  || | |||||||  |||   | ||  | |||    |  | |   |||||     ||   |            
TCATGAGGGATTTCAAGAGGTTGCAACAGGATCCACCTGCAGGCATCAGTGGTGCTCCTCAAGACAATAACATTATGCTCTGGAATGCTGTTATATTTGGgtatgctgggaaatgcatcattgtttattctttcttttgtatagtttgtgttg-ggtgttaaagatctgaatcagttgcacttatacgccttcttggttgaattgcag

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag---------
||||| | || ||||||||  ||  ||| || |||||||||||||| || |||||||||||||| |||||||| ||| ||||||||||||||||||| |||||     |  ||  || || |    ||    |  | |  |   |||  | |  ||   ||  |   || | ||    |   ||||   |  | |         
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtac----ccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt

upper sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttga--catcgt-ctttggatatgcttatttcttttacag----
||||| | || |||||||| |||   || || |||||||||||||| || ||||| |||||||| ||||| || ||||||||||||||||| ||||| |||||  | | ||   | ||| |    | |||         ||   |    | ||  |     |  |  ||  | | |||   ||   |     |  | |    
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgta--acgaagtgcctccctggtttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt

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|32807434|gb|CD959668.1|CD959668
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32797239|gb|CD949475.1|CD949475
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32799894|gb|CD952130.1|CD952130
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32807019|gb|CD959253.1|CD959253
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|211443180|gb|FL376062.1|FL376062
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32799116|gb|CD951352.1|CD951352
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32798985|gb|CD951221.1|CD951221
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGGTACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32799638|gb|CD951874.1|CD951874
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|211312738|gb|FL018802.1|FL018802
EST:     GGCGCCCCGCANGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32802786|gb|CD955022.1|CD955022
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG
EST: gi|32809657|gb|CD961891.1|CD961891
EST:     GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTATCATATTTGG                         ACCTGATGATACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgca ... tcttttacagACCTGATGATACCCCGTGGGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGGATAACAACATAATGCTGTGGAATGCTGTCATATTTGGgtatgatgcagaatccccccgcccccttttccccacttcttagtttgaattgtaatatttgacatcgtctttggatatgcttatttcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG