Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 7
gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
         | |  || | |    |   ||     |       |     | |||||  ||  | ||    | |   |   ||||  | |  ||  ||||||||||| |||||| |||| || ||||| | |||||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||| |||||||||
--------gtatggaaacttcccatgaggaggttcttccattcatatttctcttac--tttcttttcattgttctctctctcttatttg--tgtatgcagACCTCCTGAGTTGTTACTCGGGAGCACGAGGTATGGTCCAGCCGTTGACATGTGGTCAGTGGGTTGTATTTTTGCTGAGCTTCTCAATGGAAAGCCAATA

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgtt---gttgca--agcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
|||     ||  |   |||||| |     |  ||   ||    | ||| | ||| |  ||  |   |  |||  | ||  ||||    |||    |||    |||||| ||||||||||| ||||| | ||||| |||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||  |||| || || || 
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttga--acagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0141g00280.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------gtatagtattgtaaaaccatggttttgagaa----acattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
                         || |   | ||   | |     | ||| | |     |||  || ||||  |    ||  | | | ||  |  |      | | || |   | |||| ||   || || ||||| ||||| || |||  ||||||||||||||| || |||||||||||||| || || ||||| ||||| || ||| |  |||| || ||||| 
gtaaaatattacattaacctcatgtgttttaaactgcctagctcaattgttgtgcatgttgcatcttttccaagaataagct--ccgcttttcatttagttgattcaggtttatattgatttgc-atagGCCACCAGAATTGCTGCTAGGAGCCACAAAGTATGGCCCTGCTGTTGACATGTGGTCCGTCGGTTGTATCTTTGCTGAGCTTTTGTATGGAAAACCAATT

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------gtatagtattgta---aaaccatggttttgagaaac--attgt-------tgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
                                                                        |||||||| | ||   |  | | ||  |  ||| |   ||||        ||   | ||| |    ||           |  ||||  ||| |   | |      | | ||| || || ||| || || | ||   ||| |||||    |||||||| ||||||||||||||||| ||||||||||| || |||||||| ||||| || || 
gtaaggtatcagtgctctatttctgctattgatctcccgaaacatatagagctttagatgtcttctgttggggtatagtactctagttattcgacggagtatagacattgattgcgctattatgtgtagcagactacaactagcacgtcacctggctttctaatttcacttcttcctgtttcagGCCCCCTGAGCTGTTATTGGGTTCCACCAAGTACACTCCAGCCGTGGACATGTGGTCAGTGGGATGTATTTTTGCCGAGCTTCTCAACGGGAAACCCATT

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
                                                                |||| || |   ||    |  |     | ||||| | |  |   | |   |||   |   ||  |  |  | |  ||| || ||      | | ||| || || ||| ||||  | ||   ||||||||||   ||||| || ||||||||||||||||| || |||||||| || ||||| |||||||| || || 
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactg-agcataagtgagcattgctccatagtggacgactactagtaa-gtcacttgactttctagtatttctt--cctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ34303 (Selaginella moellendorffii), 3'ss of exon 5
gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
                                               |  |||      || | |||||   |  ||  |  | |     || | |  |||||||| ||| | || |||||  | ||||||||||| ||||| || ||||||||||| |||||||| || |||||||| |||||| | || |||||| | 
-----------------------------------------------gtacctagtccgtgct-ttgcagaatgtttctggttacggccgtttgttatagACCTCCTGAGCTACTTCTTGGCTGTACAAAGTATGGGCCAGCAGTAGACATGTGGTCTGTGGGCTGCATCTTTGCAGAGCTTCTCTACGGAAAGCCAGTG

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|71766382|gb|DR964319.1|DR964319
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGGCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|78078029|gb|DV506444.1|DV506444
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|149107723|gb|EE189597.2|EE189597
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|71430764|gb|DR811814.1|DR811814
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|149099519|gb|EE185557.2|EE185557
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|211438449|gb|FL012011.1|FL012011
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTTGACA
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTT-GACA
EST: gi|32844191|gb|CD983872.1|CD983872
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|148969561|gb|EE020392.2|EE020392
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|211325352|gb|FL255515.1|FL255515
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|148954879|gb|EC900358.2|EC900358
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|32845306|gb|CD984987.1|CD984987
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|149087325|gb|EE176860.2|EE176860
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|148955711|gb|EC901398.2|EC901398
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGGTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
EST: gi|149106097|gb|EE291761.2|EE291761
EST:     AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAG                         ACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT
genomic: AGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACAT

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: 419

ATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

ATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

ATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

ATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCGTGTGATCACTTTGTGGTATAGgtattgtcta ... ttggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA
    cccttac  putative branch site (score: 273)
                           ttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA

- - - - - - - - ccatggt
- - - - - - - - - - - - - gagaaaca
- - - - - - - - - - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - - - - - - -caggccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagc