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

...tccttgttgttcttaagtatagaactatatttcactctttttattcccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 7
tccttgttgttcttaagtatagaact-atatttcactctttttattcccatttctctattaggactggagaatc-taatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
||  | |  |||  ||  || ||||| | |  |     |   ||     ||||   ||||     |  |   |  || | |  | |      |  | |||||| |||||||||||||| || ||||||||||||||||||||||| |||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||
tcaatctaattc--aatcatggaacttaaaacttttgatcaatagaagtatttaaatatttaattttaatgttggtatttttctgtgtgcgcgctaatgcagGGGATTCAGAGAAGCTAGTTAAAGTTCTGTTTGAGCTTGCTAGACATCATGCACCATCGACAATATTTCTTGATGAAATTGATGCTATTATCAGCCAACG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G26100.2 (Glycine max), 3'ss of exon 2
----------------tccttgttgttcttaagtataga---actatatttcactctttttattcccatttctctattaggactggagaatctaatgtcttt----ttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
                |   |    |  |||| || | |   || |||| ||| |   ||||  |  | ||      |     ||   |  |  |  | |      || || |  || |||||| |||||||||||| | || |||||  | ||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||| ||||| || || ||
gttagttagttacccattagttcaatagttaattacatatttacaatatatcagttagtttaggctgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 7
tccttgttgttcttaagtataga---actatatttcactctttttattcccatttctctattaggactggagaatctaatgtcttt----ttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
         |  |||| || | |   || |||| ||| |   ||||  |  | ||      |     ||   |  |  |  | |      || || |  || |||||| |||||||||||| | || |||||  | ||||| ||||| |||||||||||||| || |||||||| ||||||||||| ||||| ||||| || || ||
-------aatagttaattacatatttacaatatatcagttagtttaggctgaattagtgtgttattttgtgaatacgtacatttacaaaatttattttggactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGATGAAATTGATGCAATCATTAGTCAACG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 7
tccttgttgttcttaagtatagaac-tatatttcactctt--tttattcccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
   | |||  |   |  | || ||  |||   | | | |    | | |    || || |  |  || |    |   | |       ||| | || || |||||| |||||||||||| | || |||||  | ||||| ||||| |||||||||||||| || |||||||| ||||| ||||| ||||| ||||| || || ||
--atagttaattacagatttacaatatatcagttagtttaggctgaattagtttgctattctgtgaatatgtacatttacaaaaaattcttttg-gactgcagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAACTTGCAAGGCATCATGCACCCTCAACAATATTTCTTGACGAAATTGATGCAATCATTAGTCAACG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 7
tccttgttgttcttaagtatagaactatatttcactctttttattcccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
    ||   |  ||  |||      | || |     |  |  | |   ||       ||||||      ||  |   | |||||  || | |   | |||| ||||| |||||| |  | | ||||||||| || || ||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| ||
---gtgaaatatttt-gtacctttatttactcttaaccatgaaataagatgcagtctttaggagaaataaaatttggg-cttttcaatgttt---ttcagGTGATTCTGAGAAGTTGATAAGAGTTCTGTTCGATCTAGCTAGGCATCATGCACCTTCGACAATATTTCTTGATGAGATCGACGCGATCATAAGCCAACG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 7
--tccttgttgttcttaagtatagaactatatttcactctttttattcccatttctctattaggactggagaatctaatgtcttttt-catatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
  |  ||  || | |    |||  | |  | | | |     |  | |  ||        ||| |   ||||  | | ||  |||| |   | |||   || ||| |||||||||||| | || |||||  | ||||||||||||||||| ||||| || || || ||||| ||||||||||| |||||  | ||||| || ||
gatagtttatgatatctgatatgcatccttttcttagatgatggactgtcagcaa---gttatggtgggagtgtatcattcctttatgtttttgtttatgtagGTGATTCAGAGAAGTTAGTGAAAGTGTTATTTGAGCTTGCTAGGCACCATGCCCCTTCAACTATATTTCTTGATGAAATTGATGCGCTTATCAGTCAACG

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|148995361|gb|EE034575.2|EE034575
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|211131749|gb|FL468282.1|FL468282
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|32837432|gb|CD977110.1|CD977110
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|32849820|gb|CD989501.1|CD989501
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|67012372|gb|CO441121.1|CO441121
EST:     CAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: CAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|32838514|gb|CD978192.1|CD978192
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
EST: gi|31355569|gb|CD439926.1|CD439926
EST:     AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG                         GAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG
genomic: AACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 264

ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTGgtatggcttt ... gtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG
                         atctaat  putative branch site (score: 158)
                                   tttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttgttgttcttaagtatagaactatatttcactctttttattcccatttctctattaggactggagaatctaatgtctttttcatatgtgagtgcagGAGATTCAGAGAAGCTTGTCAAAGTTCTGTTTGAGCTTGCTAGGCATCATGCACCATCCACAATATTCCTTGATGAAATAGATGCTATCATCAGCCAGCG

- - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatat