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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttctcaaactcataaacatagttttactgtttgtagttcagttgcatcagggccgtgccggtaaaatctgaggccctgtacaaattctgaaat...

Basic information

species Zea mays
transcript GRMZM2G021378_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021378_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 8
ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttctcaaactcataaacatagttttactgtttgtagttcagttgcatcag-ggccgtgccggtaaaatctgaggccctgtacaaat-tctgaaat--
|||||| |||| | ||||||| ||||||| || || ||||||||||| || ||||||||||||| | | | | ||| || | ||||| || | |   ||| || || | |||||      ||| | |   |  ||||        |||| || | ||  |||   
ACATTAAGAGAGGCAATCCAGAAGGAATACCGGGATGTAGTGGAGCGGCGCGTTTTCACTGgtcagttatgttaaattc-tcaacatggtatcaggatttctatttgaattgcactgatagccttactcttgtaatcatccattgtgtaaaattatccaaaacag
















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|78075707|gb|DV504141.1|DV504141
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|78109316|gb|DV527732.1|DV527732
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|76289341|gb|DV028909.1|DV028909
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTG-TGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|76928325|gb|DV171578.1|DV171578
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|38568867|gb|CF974752.1|CF974752
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGA
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGA
EST: gi|76289342|gb|DV028910.1|DV028910
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|78124413|gb|DV542797.1|DV542797
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGGTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|78075706|gb|DV504140.1|DV504140
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|71320028|gb|DR796779.1|DR796779
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG
EST: gi|78109317|gb|DV527733.1|DV527733
EST:     AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTG                         TGACGGGGGAGCGTGCTGATGAAGAG
genomic: AGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG

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: 35 (upstream exon), 26 (downstream exon)
Score: 5

ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG


Block sizes: 49 (upstream exon), 26 (downstream exon)
Score: 323

ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 469

ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG


Block sizes: 48 (upstream exon), 26 (downstream exon)
Score: 54

ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttc ... aaccgaacagTGACGGGGGAGCGTGCTGATGAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTACGAGAAGAAATCCAGCAGGAATATCGTGACGTAGTGGAGCGTCGTGTTTTCACTGgtccgctttctcaaactcataaacatagttttactgtttgtagttcagttgcatcagggccgtgccggtaaaatctgaggccctgtacaaattctgaaat

- - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - -  GTGGAG