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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttccatatacatgcagtccttggtttgatgccaataaaagttatctacaactcgttgggtgatcgtataagtataagcttacgacttgcaagtt...

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 5'ss of exon 20
AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttccatatacatg-cagtccttggtttgatgccaataaaagttatctacaactcgttgggtgatcgtataagtataagcttacgacttgcaagtt
|||||  |||||||| ||||| |||||||||||||||| ||| ||| |||||||||| ||||||||||| ||||||||||||||| |||| |||||||||||||  ||||||     ||   |   ||  ||| | |     ||   ||   | ||  ||  |     |   ||  | |      ||  | || | |  | 
AAATGAAGTGAAGAAAATGACACAGGAACAGATCTTAGCCTTTGAACAAAGTGGAGAAATTTCATTCTTTGGTCATTGCTTGAAGTTAGACGATATTAAGgtaacattccatgcttctgatggatgttaatttaaaggtttaaatgattgcttgcatgtcagttttgaagattaatatttggtaattgtg-ctagtatatg
















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|71432888|gb|DR813938.1|DR813938
EST:     GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAG                         GTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
genomic: GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
EST: gi|40334151|gb|CK368221.1|CK368221
EST:     GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAG                         GTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
genomic: GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAG                         GTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
genomic: GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
EST: gi|45568479|gb|CK986083.1|CK986083
EST:     GTGGAGAGATTTCATTCTCCGGTCATTGC-TGAAGCTAGATGATATTAAG                         G-TGTTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGA
genomic: GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTG-TCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGA
EST: gi|26456279|gb|CA827862.1|CA827862
EST:     GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAG                         GTTGTCCGACAATTCAAGCGTCCTGAAAACATGTCGGAGAAGGAGATTGAT
genomic: GTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
EST: gi|211108629|gb|FL325826.1|FL325826
EST:     TAGATGATATTAAG                         GTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT
genomic: TAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGAT

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: 153

AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGATGCTGCAGGAGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 72

AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGATGCTGCAGGAGATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 125

AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGATGCTGCAGGAGATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 72

AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttcc ... ttatttttagGTTGTCCGACAATTCAAGCGTCCTGAAAACGTGTCGGAGAAGGAGATTGATGCTGCAGGAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAGATTTCATTCTTCGGTCATTGCTTGAAGCTAGATGATATTAAGgtaatgttccatatacatgcagtccttggtttgatgccaataaaagttatctacaactcgttgggtgatcgtataagtataagcttacgacttgcaagtt

- - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaaa