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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggagtatttcatcacactaggatttgtgcaacactgtaaatagcatcttttttattggcttggatttggaatagcatattgacagactttattgtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G116434_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 10
gtgtggagtatttcatcacacta-ggatttgtgcaacactgtaaatagcatcttttttattggcttggatt-tggaatagcatattgacagactt-tattgtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG
|| |    ||| |  | |||||| |||| | ||||   |       |   | ||||| |  | ||   | |      || | |      | | || | || |||||||||||||| |||||||||||||||||||| || |||||||||||||| || |||||||||||||| |||| ||| || ||||||||||| || || || ||||
gtatt---tatattcttacactaaggatgtctgcagttcaaagggca-tgtttttttcagagactcaaaatgcttgctaaccttgctctacatttattttctccttgcagACACACAGGATAAAGAAGTTTGTTTTACACACAAACTTCCCTGGTCATTCAGATTTCAATTCCTATATGAAGTGTAACTTTGTTATCTATGATGCCGAAG

upper sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 10
gtgtggagtatttcatcacactaggatttgtgcaacactgtaaatagcatcttttttat-tggcttggatttggaatagcatattgacagactttattgtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG
  ||      ||| ||         |  | |  |  ||| | ||||  ||  |   ||| |  | | |   | ||| ||  | |      | | |||||   |||||||| ||||  || ||||| ||||| ||||| |||||||  ||||| ||  ||||||| |||||||| | |||||||||||||||||| || |   ||||  
--gtactcctttttattgtgtgtcaaaatatatattact-tcaataatattgtgcatatatatcatcgtacttgaa-agt-tctcagattattgtattggatttgcagACTCATAAAATCAAGAAATTTGTCTTGCACACAAACTATCCTGGGCATGCAGATTTTAATTCATACATGAAATGCAACTTTGTTATCTATGGTTCTGATT
















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|13126006|gb|BG316681.1|BG316681
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|67024702|gb|CO453451.1|CO453451
EST:     ACTTTTACAACTACTTCTCGCGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|148961880|gb|EE012666.2|EE012666
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|78074282|gb|DV502716.1|DV502716
EST:     GTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: GTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     ACTTTTACAACTACTTCTCGCGTGGAATTGATATCTTATTTAATGGACAG                         G
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcag-
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     ACTTTTACAACTACTTCTCGCGTGGAATTGATATCTTATTTAATGGACAG                         G
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcag-
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     ACTTTTACAACTACTTCTCGCGTGGAATTGATATCTTATTTAATGGACAG                         G
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcag-
EST: gi|40334237|gb|CK368307.1|CK368307
EST:     ACTTTTACAACTACTTCTCGCGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|60348112|gb|DN215085.1|DN215085
EST:     CTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: CTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|101393044|gb|EB818453.1|EB818453
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|71762669|gb|DR960606.1|DR960606
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|78106231|gb|DV524649.1|DV524649
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|78110552|gb|DV528962.1|DV528962
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
EST: gi|76014245|gb|DT941415.1|DT941415
EST:     ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAG                         ACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA
genomic: ACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCA

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), 47 (downstream exon)
Score: 124

CATACACTCCGCATCAGAAGCCAGGCCTCGGACGACCCTTTGTGGAGATTACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CATACACTCCGCATCAGAAGCCAGGCCTCGGACGACCCTTTGTGGAGATTACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 130

CATACACTCCGCATCAGAAGCCAGGCCTCGGACGACCCTTTGTGGAGATTACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

CATACACTCCGCATCAGAAGCCAGGCCTCGGACGACCCTTTGTGGAGATTACTTTTACAACTACTTCTCACGTGGAATTGATATCTTATTTAATGGACAGgtgtggagta ... gtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttattggcttggatttggaatagcatattgacagactttattgtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG
                            tattgac  putative branch site (score: 133)
                                           ttgtcctt  putative PPT
                                     actttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggagtatttcatcacactaggatttgtgcaacactgtaaatagcatcttttttattggcttggatttggaatagcatattgacagactttattgtccttgcagACACATAGGATAAAGAAGTTTGTTTTGCATACAAACTTCCCTGGCCACTCAGATTTCAATTCATATAAGAAATGCAACTTTGTTATATACGACGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG