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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG

Basic information

species Zea mays
transcript GRMZM2G009894_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
----------gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgt-ttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-
           |  |||     |  ||  |||  ||  |  ||  | ||| | | | || || |   | ||   |    |||   ||  | |   | |    | || ||  | |||| |||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||| 
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcc-cctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
                  | ||| |||||     | |  | | |   | ||  ||||  |   |  |  ||| | | | |    ||  | ||||||     |   | |   ||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||| ||||| ||| | || || ||            
------------------gttcgctctgt----gcaaattctctaacttgttctcac--tttgttgatttcctcttcatttc--gtaacattttgtgcattgaattgc---agAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
                  | ||| |||||||     |  | | |    |||  | ||  |   |   |  | | |||  |    |||     |||| ||||  ||   | | |||||||| ||||||||||||||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| ||| | ||||| ||            
------------------gttcgctctgttca----atttctctaacacgttcttacttt---tttgctgctctcttcatt---gtcttacattgtgtgcattgaattgca-gAGATGGCTAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCACAAGAATGGCATCAAAAAGCCAAAGAGGCACCGCCACACTTCCACCAA

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCG--GAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
           |  |    ||  |  |  |   || | |  |  |  |  | ||   | |   | |   ||  |  | | |   |||   |  | ||||      |     | ||||||||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| |||||||||||||| |||||| | || || ||            
-----------gttcgtttcttcaatttctgtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcagAGATGGCAAAGTCGAAGAATCACACAGCACACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G06680.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG
|| |    |    | ||||   ||||  |   ||  |  ||  || |   ||||| |  |   | |         | | | |||   |  || |||| |    | |     ||| ||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| ||||||||||| | |            
gttagctgcttata-tccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaag-

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G06700.3 (Arabidopsis thaliana), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctacta--gatgtgttg-ttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-------------
               |  |||     | |  ||||    ||| | | | ||| | | | ||     |     ||    ||    ||| | |  | |  | ||      |     ||||||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| ||              
--------------gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagagATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAG

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
|| |    |    | ||||   ||||  |   ||  |  ||  || |   ||||| |  |   | |         | | | |||   |  || |||| |    | |     ||| ||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| ||||||||||| | | | ||||| ||            
gttagctgcttata-tccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaag--ttgtgtt-gtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctacta--gatgtgttg-ttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------
               |  |||     | |  ||||    ||| | | | ||| | | | ||     |     ||    ||    ||| | |  | |  | ||      |     ||||||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| ||            
--------------gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG---------
                          |    |  ||  || | ||| |      |  || |  |    |||||   | | |||| |   |||    || ||  | |   |  || ||||| ||||||||||||||||| || ||||||||||| ||||| || |||||||| || |||||||| |||      ||||| ||          
-------------------------gtacagcctctgcatcttttggtaaa--acgacgccgtttttgctcccatct-cactgaat--tcttccactttcaatgctgtagG-GAAATGGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACC

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtc-gccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----
           |  |   | |   |  |||     | |  |  || |  ||  | | | |     |  ||||   || |    | |  |  |||  || ||  |    | |   ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |      
--------ttagttcggagatgatttagttgaattttggaggattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCAGGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacc-tcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG--------
       | ||| |      |   |    |  |    ||| | | | | ||   ||  |    | | || |    | | |  |||||    |||  || ||  |    | |   ||||||||||||| ||||| ||||| || ||||||||||| ||||||   |||||||| || |||||||||   |||   |||    |         
------gttcgg-agatgatttagttgaattttggaggat-tctgggtagttagcattggagcttctccatgtttcctgcattgagtt---tttcattcgctcgatagcagGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
-gtaactctccggcactccgctcgatctgttcctactagatg-tgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG--------
 | ||   |     | |  |   | | ||  || |     || |||||||  || |  | |||  |     ||    ||   |||| |   || | ||||    |    | |   ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     |         
agcaatagtttc-tagtgtggcagctgtggccccagggactggtgttgttgttcct--ctgtcggt----gtcttgattga-ctgatttttctgtggttttgtag----cagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG

upper sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaactctccggcactccgctcga-tctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----
       | | ||| |    || | | ||       | |       |   |   |    ||   ||   |     |||  | ||| |    |||   | |    |   | |   ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     |      
-------tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgat-tgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC

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|211369554|gb|FL313255.1|FL313255
EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCNAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|116829168|gb|EC865159.1|EC865159
EST:     TTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAA-CAGTC
genomic: TTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|211200178|gb|FL316755.1|FL316755
EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|211366908|gb|FL313254.1|FL313254
EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|116817813|gb|EC860723.1|EC860723
EST:     CGGACANTTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: CGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|211200179|gb|FL316756.1|FL316756
EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
EST: gi|211416484|gb|FL311420.1|FL311420
EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

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: 687

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1165

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 873

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 607

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG
                         cccttac  putative branch site (score: 607)
                                         ccttttgttt  putative PPT
                                           ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC