Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctccttgtagactattcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag...

Basic information

species Zea mays
transcript GRMZM5G868433_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 2
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctc-cttgtagactat-tcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag
|| ||||||||| || | ||||||| ||||||||||||||||| ||| |||||||||||| ||||||||||||||||||||||||||||||| |||||||| ||||| | || | |||| | | | | | ||| | |||| || || | ||| |||| | || || | | ||
GAGCAAGGAGAAGGCCGTCGCCGAGAAGAAGAAGTCCATCGAGAGCCGCAAGCTCATCTTCTCCCGCGCCAAGCAGTACGCCGAGGAGTACGAGGCCCAGgttagatcgttggcccccacatgatccattcccgtctcgatgttatattttgcgtggcaaag-acagcgattc-cgtgggatctgggtttggtactcccaaa

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 2
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgt---cagatctcctgatcctgctcgatctaacctccttgtagactatt-cgtgc-ggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag
| |||||||||| | || ||||||| ||||||| || |||||| ||| |||||||||||| |||||||||||||||||||| |||||||||| || ||||| |||| | | || ||| | || | | || | ||| || ||| |||| | || |||| ||| | |||| ||
CAGGAAGGAGAAGGCGCTCGCCGAGAAGAAGAAGGCCGTCGAGAGCCGCAAGCTCATCTTCGCCCGCGCCAAGCAGTACGCCCAGGAGTACGACGCGCAGgtgagcagagcaacct-ccccgctgcccgttgattcgcggaaccctgtggcgtctaggaatggttcgtttagatttgcgtt--gcgcatcgacg-catcgtgaa-
















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|15632349|gb|BI679442.1|BI679442
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173109|gb|FK956294.1|FK956294
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACARCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173107|gb|FK956292.1|FK956292
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211171435|gb|FK956283.1|FK956283
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173119|gb|FK956304.1|FK956304
EST:     GCTCATCTTCACCCGCGCCAATGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACT-GTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: GCTCATCTTCACCCGCGCCAA-GCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211171440|gb|FK956288.1|FK956288
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173114|gb|FK956299.1|FK956299
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|20301133|gb|BQ164076.1|BQ164076
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173112|gb|FK956297.1|FK956297
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|211173121|gb|FK956306.1|FK956306
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGNTACAGCTTAAGCGTNAGGCCCGTTKSGAAGGGTGGTTT
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTT-GAAGGGTGGTTT
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAG                         GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC
genomic: AGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTC

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: 701

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 841

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 575

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 343

GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctc ... ctgagagcagGAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGGAGAAGTCCCTGGCCGAGAGGAAGAAGTCCATCGAGAACCGGAAGCTCATCTTCACCCGCGCCAAGCAGTACGCCGAGGAGTACGATGCCCAGgtcagatctcctgatcctgctcgatctaacctccttgtagactattcgtgcggggtgggtcgtagggcttcgcgtgcggcgtgttattttcatctcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG