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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatattgttgtc...

Basic information

species Zea mays
transcript GRMZM2G171745_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 5'ss of exon 8
---GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatatt--gttgtc
   |||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||| ||| | | ||   | |  | |  | | | || | ||   ||   | |  |  |||||||  || |||   ||  | |   ||  | || |   |  || 
CAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg--tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G171745_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 5'ss of exon 8
GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatatt--gttgtc
|||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||| ||| | | ||   | |  | |  | | | || | ||   ||   | |  |  |||||||  || |||   ||  | |   ||  | || |   |  || 
GCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg--tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G171745_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 8
-----------GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatat--tgttgtc
           |||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||| ||| | | ||   | |  | |  | | | || | ||   ||   | |  |  |||||||  || |||   ||  | |   ||  | || |   |  || 
AATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg--tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

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|89251568|gb|DY623354.1|DY623354
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|86472724|gb|DY239094.1|DY239094
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|32809485|gb|CD961719.1|CD961719
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|50339562|gb|CO534688.1|CO534688
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCCCCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|60340320|gb|DN207293.1|DN207293
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|74242378|gb|DT650292.1|DT650292
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|67021266|gb|CO450015.1|CO450015
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|28986944|gb|CB351386.1|CB351386
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|76931005|gb|DV172591.1|DV172591
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|211192853|gb|FL432744.1|FL432744
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA

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), 45 (downstream exon)
Score: 103

GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCAGAATGGGACCTGCTGATACCTTGATTGAGACATTTTGACGCCGGAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCAGAATGGGACCTGCTGATACCTTGATTGAGACATTTTGACGCCGGAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCAGAATGGGACCTGCTGATACCTTGATTGAGACATTTTGACGCCGGAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCAGAATGGGACCTGCTGATACCTTGATTGAGACATTTTGACGCCGGAGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatattgttgtc

- - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA