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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctctatgttcctcagtaagtatgtgtacttttcctgtgtccgaacctgactaacctatcattcataatacctggacactgcag

Basic information

species Zea mays
transcript GRMZM2G008209_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008209_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g07880.1 (Oryza sativa), 5'ss of exon 9
AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctctatgttcctcagtaagtatgtgtacttttcctgtgtccgaacctgactaacctatcattcataatacctggacactgcag---------------------------------------------------------------------------------------------
|||| | || |||||||||||||||||||| ||||| || |||||||||||||| ||  | ||| | ||||||||| | |||||||||||||||||||||||||| |  ||||   |    |  |   | |     |   ||  |  || ||   |     || |   | ||   | |   ||                                                                                                  
AGCAAGTGGTCCTTTGAACATGCAACTCAATCAAGTTCCGAAGATGCTTTTCATTCTGAGAAAACAATGGGCTCCTTCAGCATTTTGTGTATCCTTCAAGgttagtttgatgtattttcacacttccatatggagctatggttgctcaagcttttttctgcattaaagaaaacctcagtgtaccttcattctgctcgtgttactctcgaaatatcttattttctagagtcgagatgactagacccaccttactgctggcgcctaatacctgcacattacag
















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|78110994|gb|DV529391.1|DV529391
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|71318838|gb|DR796180.1|DR796180
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|86469977|gb|DY236347.1|DY236347
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|18168718|gb|BM338558.1|BM338558
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|74246159|gb|DT654073.1|DT654073
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|71307842|gb|DR790142.1|DR790142
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|89249896|gb|DY621682.1|DY621682
EST:     TCATCCTCCGGAAAAAATGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTTTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|71756861|gb|DR954798.1|DR954798
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTCCAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|74243665|gb|DT651579.1|DT651579
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
EST: gi|78120327|gb|DV538711.1|DV538711
EST:     TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAG                         CTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG
genomic: TCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAG

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: 39 (upstream exon), 46 (downstream exon)
Score: 53

AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAGAAGTACGGTATGAACGTCGTGGTGGCAAATGAACTCGCAAACTACAAAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 72

AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAGAAGTACGGTATGAACGTCGTGGTGGCAAATGAACTCGCAAACTACAAAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 63

AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAGAAGTACGGTATGAACGTCGTGGTGGCAAATGAACTCGCAAACTACAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 73

AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctcta ... gacactgcagCTCGAAACAGATCCTAACATTCTCCTACAGAAGGCAGAGATGGCTTTGAAGAAGTACGGTATGAACGTCGTGGTGGCAAATGAACTCGCAAACTACAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGGCGGCCCTTTGAACATGCAACTCAACCAAGTCCCTAAGATGCTTTTCATCCTCCGGAAAAACTGGGCTCCTGCTGCATTTTGTGTATCCTTCAAGgttagctctatgttcctcagtaagtatgtgtacttttcctgtgtccgaacctgactaacctatcattcataatacctggacactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC