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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

Basic information

species Zea mays
transcript GRMZM2G465333_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
               |  || | | | |||||| |        |  ||| || |  ||    ||  |  |||||    |   ||  ||  |   | |  |||    |||| |||||||| || || || |||||||| |||||||||||||  || ||||||||| | ||||||||||| |||||||| || ||| | ||||| ||||
---------gttagcatttgacatctatttattttgaagaacttttcattgt-ttcatctatttcgtacttgtcaatattgaatt-tatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtaattcaccacgcaaact-ggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
    ||  ||   |    | | |  | | ||||| |||  | | |   | |||    |        ||||| | |||    | |     || |  |||   | |    | |||||  |||||||||| || ||||| |||||||||||||| ||    ||||||||||| || || || || ||||| |||||||||||  | ||||| ||| 
gtttgtgttttctctttaatattcagtcaatcttaatt--tcttttattcacacatcagg------ctttaatattgatctgttttggggacatttgc---tttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctt-tattgttgtctggctaa-----catgataaatgcacatatttttc----ccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
                |   |      | | | |  ||| |   |     || |       | |  |   | |   ||  | ||||  ||    | |       |  |||   |   ||||  |      |||||  |||||||||| || || |||||||| ||||||||||| |  ||||| ||||| ||||| || |||||||| ||||| || ||| | ||||| ||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtaattcaccacgcaaact--ggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttc--ccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
                     ||   | ||     |   |      |     ||||||   ||   ||| ||    | | || ||| | ||    |||    ||     |  |      | ||| |    ||||| || ||||||||||||||||||||||||||||||||||| |  |||||||| || || ||||| |||||||| ||||| |||||  | || || || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctt-tctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
 ||   |  ||  |    | ||  ||  |   | || | |      | ||  || |   |  || | |    |     |||| | ||       | |     |  ||||| || ||||| ||||||||||| |||||||||||||||||    |||||||| ||||| || ||||||||||| ||||| |||||  | || || ||  
-tataccttcaatctttatcgcagattctacatattctttcagatccttgagatgtcagaatttcaatagcttgcaagtaacttcat-------cgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
                                           |||  | |  |   |       |  |      | ||||| |      ||      || || ||||||||||||||| ||||| ||||| || |||||||||||||||   || |||||  || |||| || ||||||||||||||||||||| | || |||||||
------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttctg-----gttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
                                         |||  | | ||| ||   |     | |   ||||  ||    |  |         | || || |||||||||||| || ||||| ||||| || |||||||||||||||   || |||||  || |||| || ||||||||||||||||||||| | || |||||||
-------------------------------------gtaagcttgcgtagtagatgaaagag--aatagagtctaacttcgctcct---------tgttctttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|9732524|gb|BE511276.1|BE511276
EST:     TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAAT                         ATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
EST: gi|32936343|gb|CF041155.1|CF041155
EST:     TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAAT                         ATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
EST: gi|211155649|gb|FL446891.1|FL446891
EST:     TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAAT                         ATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
EST: gi|211435454|gb|FL453398.1|FL453398
EST:     TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAAT                         ATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGAC

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: 951

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 579

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGTGTCACTGTGAAGAAAAGCAAGAATgtaattcacc ... tttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC
                      ggctaac  putative branch site (score: 579)
                                           tatttttccc  putative PPT
     tatctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC