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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcaccacttgtgcgaacagcttcagttctcttaaaacgaaaaaaaacactagactacgttatgtgaaccgaaaactctttattgtctttaaactgtacataagttttttagattccccattagacaagttttcagtagtgacacatggcatgcag

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 5'ss of exon 11
GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcaccacttgtgcgaacagcttcagttctcttaaaacgaaaaaaaacactagactacgttatgtgaaccgaaaactctttattgtctttaaactgtacataagttttttagattccccattagacaagttttcagtagtgacacatggcatgcag
|||  || |||||| ||| | |||||||||||||| || ||||||||||| || |||||||| |||  ||||||||||||||||  |||  | || | |       ||  |    || |    |        |||| |  |  || ||   |   |    ||  | || |                                                                       
GGATCAGCGAACCAGTACTCCGGAATTGTAAGCTGCGCCCAGACAATCCTGAGGGAGGAAGGACCTGGGGCATTCTTGAAGgta--gcaaaatttttcc-------tttcgcctgctgatggtggtgggtg-cactggggt-tgtgattgaacttggtggctggtgatggcag--------------------------------------------------------------------
















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|28984641|gb|BQ539144.2|BQ539144
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|28983266|gb|BQ539448.2|BQ539448
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCATAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     GCTGTGTTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTTTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|16927262|gb|BM080331.1|BM080331
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|71302081|gb|DR787128.1|DR787128
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|78092776|gb|DV521150.1|DV521150
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     TCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAAGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTCTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATCGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|113702087|gb|EE679591.1|EE679591
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|50325363|gb|CO520489.1|CO520489
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAAGCATTGTTGAAG                         GGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT
genomic: GCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTT

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: 38

GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTTGGCATGCTGGAGAAAACCAAGTCGATGCTAGCCGAGAGGAGGAACCGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63

GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTTGGCATGCTGGAGAAAACCAAGTCGATGCTAGCCGAGAGGAGGAACCGCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 52

GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTTGGCATGCTGGAGAAAACCAAGTCGATGCTAGCCGAGAGGAGGAACCGCG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 14

GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcacc ... tggcatgcagGGCATTGAGCCGCGAGTGCTGTGGATTGGCATCGGTGGGTCCATCTTCTTTGGCATGCTGGAGAAAACCAAGTCGATGCTAGCCGAGAGGAGGAACCGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACAAGGGAACCAATACACTGGAATTGTAAGCTGTGCTCAGACAATCCTCAGAGAGGAAGGCCCTAAGGCATTCTTGAAGgtaaagcaccacttgtgcgaacagcttcagttctcttaaaacgaaaaaaaacactagactacgttatgtgaaccgaaaactctttattgtctttaaactgtacataagttttttagattccccattagacaagttttcagtagtgacacatggcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG