Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatgatagaagcactcaaaatgtttg...

Basic information

species Zea mays
transcript GRMZM2G151009_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctgg-ccgttatatttctccgtccaatttcatttta-attctctatggcta-tgtttagga-----aaaatattatatgatagaagcactcaaaatgtttg
|||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||||||  |||| ||||||||||||||||||||  |   |  |||  | |   | |||| ||  ||| || |  ||   ||||      ||||||      |   || | | |  | | | ||||||        
ACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCAAACAGCTTACTCGCAACAGGAAGTTCCTTGTTGTAGTTCCTGTTGTCCTgtaagtattcttctattacttcttagcatccatttcaattatacaaacttattggcgggcacttaggatttaggagcaataacaggcaacatgtactcaa--------

upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatga---tagaagcactcaaaatgtttg
|||| || || ||||| | ||||||||||||||| ||  | |||||||| || |||||||||||||| |||||||| ||||  ||||||||| | || |||||||| ||  |   | |  ||  || ||   |||   |  ||   | | ||  | || | | |  | |   | |||||   |    |||| |    | | | 
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttct--ctaatttgcttg-ccatcatgtttatatacaaaggtatctgcttctggtgatgtcatagggtctatgaatgtgtgtgcacccttgttatata

upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G02540.1 (Glycine max), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatga---tagaagcactcaaaatgtttg
|||| || || ||||| | ||||||||||||||| ||  | |||||||| || ||||||||||| || |||||||| ||||  ||||||||| | || |||||||| ||  |   | || ||  || ||   |||   |  ||   | | ||  | || | | |  | |   | ||| |   |    |||| |    | | | 
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGGAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttct--ctaatttacttg-ccatcatttttatatacaaagttatctgcttctggtgatgtcatagggtctataaatgtgtgtgcacccttgttatata

upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G05940.1 (Glycine max), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatgatagaagcactcaaaatgtttg---
|||| || || ||||| | ||||||||||||||| ||  | |||||||| || |||||||||||||| |||||||| ||||  ||||||||| | || |||||||| ||     ||  ||  |  | |    |||   |  ||   | | ||  | |  | | |  | | | | ||||| ||      |      ||      
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttgcatgccatcatt---tttatatacaaaggtatctgcttctagtgatgtcatagagtctatgaaagtgtgcgtgtgtgcgtgcaccc

upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G42000.1 (Arabidopsis thaliana), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggccgttatatttctccgtccaatttcattttaattctctatggcta--tgtttaggaaaaatattatatgatagaagcactcaaaatgtttg
| || ||| | || || | |||||||||||||||||| || || |||||||| |||||||| |||||| | || || ||||  ||||||||||||||| ||||||| |   |  | |||| ||        ||||  ||||   ||   ||  ||   || |   |   | |||   |  || |||   || |   | ||| 
ATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCAAGCAGCTTACACGTAATCGCAAATTTCTCACCGTTGTTCCTGTTGTCTTgtaagttccttctctcatatctcattag--gattttgttttgcatcatcatctcttgttgatcttgttcagtatcgaaaaattgaatgccttaccttatttt

upper sequence: GRMZM2G151009_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 5'ss of exon 2
ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctggc-cgttatatttctccgtccaatttcattttaattctctatggctatgtttaggaaaaatattatatgatagaagcactcaaaatgtttg
|||| ||||| |||||    || ||||||||||||||||||||||||||  |||||||||| || ||  | || || || |   | ||||||||||| |||||||| |  || | || |   ||    ||  |   |  ||   |  |      |||| |||    |  | ||||| |  |  |    |  | | |  |||
ACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTCAACAGCTTACCCGCAACCGCAAATTTCTTACCCTAGTTCCTGTTGTTCTgtaagtcccagcaccttgttcctcaaaatctcaccactcttgtctatttccaatctatattttcttagcaaattattttctttagctgcatata-tccttg

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|211256578|gb|FL391908.1|FL391908
EST:     AAACAGCTTACTCGTAATAGGAAGTCCCTCATTGTTGTTCCTGGTGGCCT                         GAATCTGAAAGCTTTGC
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGC
EST: gi|40336961|gb|CK371031.1|CK371031
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|87157542|gb|DY402331.1|DY402331
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|211403609|gb|FL421570.1|FL421570
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGGTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGC
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGC
EST: gi|16925050|gb|BM078118.1|BM078118
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|101401475|gb|EB822417.1|EB822417
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18174920|gb|BM350308.1|BM350308
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|32846272|gb|CD985953.1|CD985953
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|26558414|gb|CA830649.1|CA830649
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACA
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACA
EST: gi|32919445|gb|CF024257.1|CF024257
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18173179|gb|BM348567.1|BM348567
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|71763891|gb|DR961828.1|DR961828
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18176788|gb|BM351721.1|BM351721
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|32939394|gb|CF044213.1|CF044213
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|71441911|gb|DR822961.1|DR822961
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18166463|gb|BM336302.1|BM336302
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|22546072|gb|BU098393.1|BU098393
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18166011|gb|BM335850.1|BM335850
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|18164494|gb|BM334333.1|BM334333
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGTTTTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|211108187|gb|FL481526.1|FL481526
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|60343697|gb|DN210670.1|DN210670
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
EST: gi|71763892|gb|DR961829.1|DR961829
EST:     AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCT                         GTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT
genomic: AAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCTCAATACCCTTGCCGTCAGCGTGCTTGTGGTCGCCAAACTACCGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCTCAATACCCTTGCCGTCAGCGTGCTTGTGGTCGCCAAACTACCGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCTCAATACCCTTGCCGTCAGCGTGCTTGTGGTCGCCAAACTACCGAATATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 126

ACCAGGGAATGTACAACACATTGACTTGGTGGGAACAAATGGACAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCCTGTTGTCCTgtaagtgctg ... tccttaccagGTATCTGATAGCTTTGCACACCACAGACTACCAACAACCTATGCTCTTCCTCAATACCCTTGCCGTCAGCGTGCTTGTGGTCGCCAAACTACCGAATATG