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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggacatatggttgcctacatcagatcattaaactggatttcttaacagttttttctttcgcagattcacattatgtcctatatgattgcattatttgtcatttagagagctgatgcgagccaaaatttaatcctctatttttttcttgtttccttctcaattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 3'ss of exon 7
gtatggacatatggttgcctacatcagatcattaaactggatttcttaacagttttttctttcgcagattcacattatgtcctatatg-attgcattatttgtcatttagagagctgatgcgagccaaaatttaatcctctatttttttcttgtttccttctcaattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG
                                                                         ||  |  | |   |  | |  |||||||||  || |  || |||||  |||  ||||||| |||   |  | | |   ||||               ||||||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| || |||
-----------------------------------------------------------------------gtatggttgcttggctacactttattatttgttcttcactgaactgatatgagt-aaaatttgatctcgttatatctgtctgttctt----------acagAGGGAAAGGATGAGCAGATTGATCTGGAGGTGTTCAACTTCACTGGTGCTGGAGGAGTTGCTTTGTCTATGTACAACACTGATGAG
















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|211440945|gb|FL371134.1|FL371134
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211423961|gb|FL408856.1|FL408856
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|148957374|gb|EC903424.2|EC903424
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGGCT
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTG-CT
EST: gi|6695772|gb|AW288850.1|AW288850
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGA-GAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|33101480|gb|CF061440.1|CF061440
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGT
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGT
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGC
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGC
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AAGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|32845300|gb|CD984981.1|CD984981
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|60343928|gb|DN210901.1|DN210901
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|67023195|gb|CO451944.1|CO451944
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|6695773|gb|AW288851.1|AW288851
EST:     AGCTACCGATGCAG-TCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|13198145|gb|BG354175.1|BG354175
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|32844807|gb|CD984488.1|CD984488
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|32844692|gb|CD984373.1|CD984373
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGACCAGATTGATCTGGAGGTATTCACCTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|211197469|gb|FL425784.1|FL425784
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTG
EST: gi|32940854|gb|CF045673.1|CF045673
EST:     AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTG                         AGGGAAAAGAAGAACCAGATTGATCTGGAGGTGTTCAACTTCACTGGTGCT
genomic: AGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAAC-AGATTGATCTGGAGGTATTCAACTTCACTGGTGCT

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: 174

TGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

TGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 782

TGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 789

TGGACTAAGCCCATCTGCATTGGAAGGCATGCCTTCGGTGATCAATACCGAGCTACCGATGCAGTTCTGAAGGGGCCTGGGAAGCTGAAGCTAGTTTTTGgtatggacat ... caattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgagccaaaatttaatcctctatttttttcttgtttccttctcaattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG
            atttaat  putative branch site (score: 789)
             tttaatcctctatttt  CT-rich tract
         aaaatttaatcctcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggacatatggttgcctacatcagatcattaaactggatttcttaacagttttttctttcgcagattcacattatgtcctatatgattgcattatttgtcatttagagagctgatgcgagccaaaatttaatcctctatttttttcttgtttccttctcaattggtagAGGGAAAAGAAGAACAGATTGATCTGGAGGTATTCAACTTCACTGGTGCTGGAGGAGTTGCCTTGTCTATGTACAACACCGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG