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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgctatgcagcacttgctgctggtagtgtacctgtatattatcttttgtaatgctggtaccatgtatgcaatgttgaaaacctggaatttagaat...

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 5
TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgct-------atgcagcacttgctgctggtagtgtacctgta-tattatcttttgtaatgctggtac-------catgtatgcaatgttgaaaacctggaatttagaat--------------
||||| || |||||||| ||||| || |||||||||||||| ||||| |||||| ||||||||||||| || ||  | || |||||||  |||||||||       ||||||| |||||||    || | |     || ||  || || || ||||||| |||       |||||    |   ||   || |   | || |  ||              
TATCTGCCAATTGAAGGCTTAGCTGCATTTAACAAAGCAACTGCAGAACTATTGTTTGGAGCTGATAATCCAGTACTCAAGCAAGGACGTgtatgtgctgtggcctatgcagctcttgctgtacttattttgtaaatactaagattttctggaatgctgctacagcgaagcatgtccttatatttagtaaacattatttaatgataattccttctgtag
















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|32863795|gb|CF003477.1|CF003477
EST:     AACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: AACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|32802835|gb|CD955071.1|CD955071
EST:     TAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: TAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|5342983|gb|AI795288.1|AI795288
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|71440750|gb|DR821800.1|DR821800
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|13515691|gb|BG517967.1|BG517967
EST:     GAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: GAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211240361|gb|FL028797.1|FL028797
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGA
EST: gi|149107658|gb|EE189537.2|EE189537
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211235886|gb|FL028771.1|FL028771
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|78104308|gb|DV522726.1|DV522726
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|76289791|gb|DV029359.1|DV029359
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211140308|gb|FL028753.1|FL028753
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|32788347|gb|CD940583.1|CD940583
EST:     TAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: TAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|148941508|gb|EC886438.2|EC886438
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211240365|gb|FL028801.1|FL028801
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACT
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACT
EST: gi|78114229|gb|DV532618.1|DV532618
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211235884|gb|FL028769.1|FL028769
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|149000841|gb|EE038069.2|EE038069
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211139377|gb|FL028748.1|FL028748
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGC
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGC
EST: gi|211140317|gb|FL028762.1|FL028762
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211238126|gb|FL028786.1|FL028786
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|71767561|gb|DR965498.1|DR965498
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
EST: gi|211139376|gb|FL028747.1|FL028747
EST:     CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTG                         GTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA
genomic: CAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCA

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: 48 (upstream exon), 47 (downstream exon)
Score: 69

TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 409

TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 48

TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 349

TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgcta ... tcttttgcagGTTGCTACACTTCAGTCTCTCTCGGGCACTGGATCACTGCGTCTCGCTGCAGCATTCATACAAAGATACTTTCCTGAAGCTAAAGTGCTGATATCGTCGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCTTCCCATTGAAGGTTTAGCCGCGTTTAACAAAGCAACAGCAGAGCTATTGCTTGGAGCTGATAACCCTGTTATTAATCAAGGACTGgtatgtgctatgcagcacttgctgctggtagtgtacctgtatattatcttttgtaatgctggtaccatgtatgcaatgttgaaaacctggaatttagaat

- - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT