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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgaatcagaatcagtttctcaaatcgtttgtcaggattccaatctaatcgcattacacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG

Basic information

species Zea mays
transcript GRMZM2G166035_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 4
gctgaatcagaat-cagtttctcaaatcgtttgtcaggattccaatctaatcgcatt----acacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
| |  ||   | | ||  || ||  |     |  ||||||| ||   || |   |||    |||  | ||  | |  || || |||  ||  ||    | |||||||||||| |||||||||||||||||||| || ||| |||||||||| |||||||||||||| || |||||||| || ||||||||||
ggtacatggcagttcaaattatctgaa----taacaggatttcatattagtattatttaacacatgttaatcaatc-ataatatttctcctgtccacccttgcagCAATTGCAGTTTCAAGGGATCACAAACCCGACCAGTCAGATGAGAGACAAAGAATTGAGGACGCTGGGGGCTTCGTGATGTGGGCTG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
gctgaatcagaatcagtttct-caaatcgtttgtcaggattccaatctaatcgcattacactt--caacaattttatgatgttttccccatcttgacctgc---agCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
       ||      |||  |    |||   | | |||       | ||| |    ||   ||   |   | |  ||  | || | || ||  ||   | |   ||| ||||| |||||  | ||||||||||| || || || |||||||||||||| ||||| || ||||| ||||||||||||||||| |
------gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 5
------gctgaatcagaatcagtttctcaaatcgtttgtcaggattccaatctaatcgcattacacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
       ||   |  |  || |||   |||||   ||  ||   |||  |   | | | ||      | |   |||||    |   ||     | |   | |  ||| ||||| |||||  | |||||||| || || || || |||||||||| ||| ||||| |||||||| || ||||||||||||||||
gtttgtacttcttgtgcttctgttga-caaattactt--caaccttctga---atttgaatggtgacttatatattttgctttcccttttttttttcctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGTTTTGTTATGTGGGCTG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
gctgaatcagaatcagtttctcaaatcgtttgtcaggattccaatctaatcgcattacacttcaacaatttt---atgatgttttccccatcttga---cctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
      |  |      | |     |||   ||| ||        | ||| |    ||   || || | ||     ||  | || | || ||  ||    |||  ||| ||||| |||||  | |||||||| ||||| || || |||||||||||||| ||||| || ||||| |||||||||||||||||||
-----gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatg-ttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 4
gctgaatcagaatcagtttctcaaat-cgtttgtcaggattccaatctaatcgcattacacttcaacaat---tt---tatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
      ||| | |  ||   ||   | | | |||    |      |  |  |   | | |||| ||   |   ||   |||  |  |||||   ||||  | |  ||| ||||| |||||  |||||||||| || ||||| || |||||||||| ||| ||||| |||||||| |||||||||||||||||||
------tcatagtttgtacttcttgtgcttctgttgataaattgcttcagccttctga-acttgaatggtgacttaaatatttttctttccttttctttccttctagCCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAAGGATTGAAGATGCAGGTGGCTTTGTTATGTGGGCTG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
gctgaatcagaatcagtttctcaaa-tcgtttgtcaggattccaatctaatcgcattacacttca--acaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
 |  | | | |||||  |  |     | |||  | |   || ||||  | ||||  |    |  |    | |  | |||| ||||       ||| |    ||| ||||| || ||  | |||||||| |||||||| |  || ||| | |||||||||||||||||||| || ||||| ||||||||||
acatacttataatcacatgatagcccttgttcatgaaatttgcaata-agtcgctctgttttgtatggtactaatttgatatttttttttgtttgtc--aaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG

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|19350739|gb|BM895271.1|BM895271
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     TGTTGCAAATGTTGGAGATTCTAGAGCTGNTATTTCTAAAGGAGGACAGG                         CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
EST: gi|31359010|gb|CD443367.1|CD443367
EST:     TGGTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGGCANG                         CGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAA

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: 509

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 589

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 558

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 350

GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttac ... tgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatcgcattacacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
                                          tcttgac  putative branch site (score: 350)
                               tgttttccccatctt  CT-rich tract
                     aattttatgatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgaatcagaatcagtttctcaaatcgtttgtcaggattccaatctaatcgcattacacttcaacaattttatgatgttttccccatcttgacctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG