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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgtattcaaatatgcaaagaatattgttagtgcatctgaactgatgactgtttattgattgctgccatggtaatatagttggtgaatttaccaaaccataaatgttatgtttgagcactcattactcaacatacctttgatatgttatggatgcttgtag

Basic information

species Zea mays
transcript GRMZM2G060872_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060872_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g06230.1 (Oryza sativa), 5'ss of exon 4
ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtaccttt----gtattcaaatatgcaaagaatattgttagtgcatctgaactgatgactgtttattgattgctgccatggtaatatagttggtgaatttaccaaaccataaatgttatgtttgagcactcattactcaacatacctttgatatgttatggatgcttgtag
   || | | ||  ||||||| || || |||||||||||||| |||||  |||| |||||||   | |||||||||||||| || ||| |||||||||||||||||||     |||  |||||||||||  | |   ||||| |      | | ||      |||  | ||| ||  || |  | || ||  |  || ||| ||     |||| |                                                        
GAGGAAGGATCAACCTCATCTTGCCATCTTGATGGATTTTGAAAGTGCCCGTCCTGCAAGAATAGCCATTAGATCACAAGCAGATGCTATGCAGTTACAGgtacctttctgtctatctaaatatgcaaaacaaacccttagttcc-----atttata-----ttacagcttgttgagatagacagattgtatggaaagttagca-----taaacg--------------------------------------------------------
















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|76292893|gb|DV032461.1|DV032461
EST:     TC-AGCAAGAAAGACTATTAGATCANCA-GCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTT
genomic: TCCAGCAAGAAAGACTATTAGATCA-CAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTT
EST: gi|16925398|gb|BM078466.1|BM078466
EST:     GCTGAAGCTTTGCAGTTACAG                         GAAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATG
genomic: GCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagG-AATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATG
EST: gi|76292892|gb|DV032460.1|DV032460
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|60355013|gb|DN221986.1|DN221986
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|37385142|gb|CF629692.1|CF629692
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|67011991|gb|CO440740.1|CO440740
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|15053917|gb|BI359462.1|BI359462
EST:     AAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: AAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|31361583|gb|CD445940.1|CD445940
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|31357257|gb|CD441614.1|CD441614
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|31362329|gb|CD446686.1|CD446686
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|149005250|gb|EE039797.2|EE039797
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|211016160|gb|FL466960.1|FL466960
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|78074389|gb|DV502823.1|DV502823
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|60341190|gb|DN208163.1|DN208163
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|211371777|gb|FL295098.1|FL295098
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|71308132|gb|DR790295.1|DR790295
EST:     TCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: TCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|60350586|gb|DN217559.1|DN217559
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
EST: gi|40335517|gb|CK369587.1|CK369587
EST:     GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAG                         GAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG
genomic: GTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGG

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: 18 (upstream exon), 32 (downstream exon)
Score: 1

ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGGGAGTGTCCAAGTCATGCTGACATTGATGAGAGGACAGATATATGGTCTT


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 8

ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGGGAGTGTCCAAGTCATGCTGACATTGATGAGAGGACAGATATATGGTCTT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 19

ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGGGAGTGTCCAAGTCATGCTGACATTGATGAGAGGACAGATATATGGTCTT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 32

ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgt ... atgcttgtagGAATGGGCTTCAGAGCACTGTTCTTCTCATTACCGTGCCCCCGAACTATGGGAGTGTCCAAGTCATGCTGACATTGATGAGAGGACAGATATATGGTCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAGGAAGCAGTCTCATCTAGCAATTTTGATGGATTTTGAGAGTGCTGGTCCAGCAAGAAAGACTATTAGATCACAAGCTGAAGCTTTGCAGTTACAGgtacctttgtattcaaatatgcaaagaatattgttagtgcatctgaactgatgactgtttattgattgctgccatggtaatatagttggtgaatttaccaaaccataaatgttatgtttgagcactcattactcaacatacctttgatatgttatggatgcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC