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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccactatttatcagccttttttttctttcagatgaaaactattcacttccatcattaaaccattagatcatcacttatttatatgatacattggtgatacctttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG

Basic information

species Zea mays
transcript GRMZM2G163233_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163233_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g36465.1 (Oryza sativa), 3'ss of exon 4
gtatgccactatttatcagccttttttttctttcagatgaaaactattcacttccatcattaaaccattagatcatcacttatttatatgatacattggtga--tacctttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG---------------------------
                                   |  | |||||| | |  | |   ||      |  | | |    || ||   |   |    ||    |  | ||||||||||||| |||||||||||| ||||||||||| || ||| | ||||| ||||||||||| || || || |||||| ||||                           
-----------------------------------gtgggaaactagttatctgcgatat-ggttaaacaaaactcttctgatgagttacacctgttaaataattgcctttgttttcagTAAATCCTAAACGAGCAGCACTGTTCTATGATAACTCTCTCTCTGGTGAAGACATCTACGACCCTTTCCTAAGTTAAGTATTCTAGAATTGTATATGTTC
















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|32864578|gb|CF004260.1|CF004260
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTTATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGACCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|211500670|gb|FL332346.1|FL332346
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTTATGAAATGCTTGCAA                         CAAATCCTAAACGTGCAGCACTGTTTTACGACCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|67023139|gb|CO451888.1|CO451888
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGACCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|211378522|gb|FL350956.1|FL350956
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|71757599|gb|DR955536.1|DR955536
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|211460866|gb|FL363678.1|FL363678
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|211207688|gb|FL307218.1|FL307218
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG
EST: gi|211155631|gb|FL334256.1|FL334256
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGA                         CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTG
EST: gi|211432573|gb|FL331494.1|FL331494
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTTATGAAATGCTTGCAA                         CAAATCCTAAACGTGCAGCACTGTTTTACGACCAATCTCTGTCTGGTGAA
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAA
EST: gi|211220146|gb|FL315335.1|FL315335
EST:     GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTTATGAAATGCTTGCAA                         CAAATCCTAAACGTGCAGCACTGTTTTACGACCAATCTCTGTCTGGTGAAG
genomic: GGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAG

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), 48 (downstream exon)
Score: 137

GGACCAGCATATGTCCGAGTTTTCCTGAATATCCTGTGGAGCATCTCCAAGGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 195

GGACCAGCATATGTCCGAGTTTTCCTGAATATCCTGTGGAGCATCTCCAAGGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

GGACCAGCATATGTCCGAGTTTTCCTGAATATCCTGTGGAGCATCTCCAAGGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GGACCAGCATATGTCCGAGTTTTCCTGAATATCCTGTGGAGCATCTCCAAGGAAGAGACTGTTGAATACGTGCTTGCCCTCATTGATGAAATGCTTGCGAgtatgccact ... ttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccattagatcatcacttatttatatgatacattggtgatacctttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG
                                          cctttgttttc  CT-rich tract
                 ttatttatatgataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccactatttatcagccttttttttctttcagatgaaaactattcacttccatcattaaaccattagatcatcacttatttatatgatacattggtgatacctttgttttcagCAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA