Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcaccgtcccccgatccggccgccgccggggccgacctcgcccgctggatccgcgctgactcgattcgtgcaccgtgcttggccgcggccctcctcttgttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG

Basic information

species Zea mays
transcript GRMZM2G069174_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069174_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g30430.1 (Oryza sativa), 3'ss of exon 1
gtaagctcaccgtcccccgatccggccgccgccggggccgacctcg--cccgctggatccgcgctgactcgattcgtgcaccgtgcttggccgcggccctcctcttgttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG
                              |   | ||   ||||    || |  |||||||     || ||| || ||     ||||| |   |   |   ||  |    | ||||||||| ||||| |||||||| ||||||||||||||| |||||||||||||||| |||||| |||||||||||||||| |  ||| || |||| |||||||
------------------------------gtaagcgcgcgcctctactcctcctgatccgcc---gcttgatccgggc-----gcttgactcagattcgtttcgcgc-gcgcgcagGTGGGGAACGCGTTCGTGCACCAGTACTACAACATCCTGCACCAGTCGCCGGATCTCGTCCACCGCTTCTACCAGGACGGGAGCCGCATCGGCCGCCCCG
















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|37418350|gb|CF646843.1|CF646843
EST:     CGCCCCCTGCCGCAGCCGCGGCATGTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|211305900|gb|FL324273.1|FL324273
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|37425819|gb|CF650658.1|CF650658
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|78109549|gb|DV527965.1|DV527965
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCCTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|149015208|gb|EE044992.2|EE044992
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|50337377|gb|CO532503.1|CO532503
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|89249461|gb|DY621247.1|DY621247
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|88752993|gb|DY537134.1|DY537134
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|101391403|gb|EB817636.1|EB817636
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|71310294|gb|DR791439.1|DR791439
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|33467081|gb|CF244130.1|CF244130
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|50324320|gb|CO519446.1|CO519446
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|211216044|gb|FL339267.1|FL339267
EST:     CCCCCTGCCGCAGCCGCG--ATTNCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGC-TTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CCCCCTGCCGCAGCCGCGGCAT--CTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|89756695|gb|DY686633.1|DY686633
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
EST: gi|50329790|gb|CO524916.1|CO524916
EST:     CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTG                         GTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG
genomic: CGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCG

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), 49 (downstream exon)
Score: 66

TCCTCGCAAAACCCTAACCCCTCGATCTCCCAAGATGGCGTCGCAGCCGCCGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 35

TCCTCGCAAAACCCTAACCCCTCGATCTCCCAAGATGGCGTCGCAGCCGCCGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

TCCTCGCAAAACCCTAACCCCTCGATCTCCCAAGATGGCGTCGCAGCCGCCGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 64

TCCTCGCAAAACCCTAACCCCTCGATCTCCCAAGATGGCGTCGCAGCCGCCGCCCCCTGCCGCAGCCGCGGCATCTGGAGCTCCGCCGCCGGCACAAGTGgtaagctcac ... ttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgactcgattcgtgcaccgtgcttggccgcggccctcctcttgttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG
 cgctgac  putative branch site (score: 64)
                                  ccctcctcttgttat  putative PPT
                                          ttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcaccgtcccccgatccggccgccgccggggccgacctcgcccgctggatccgcgctgactcgattcgtgcaccgtgcttggccgcggccctcctcttgttatgtgcagGTGGGCAACGCCTTCGTGCATCAGTACTACAACATCTTGCACCAGTCGCCGGAGCTCGTCTACCGCTTCTACCAGGAGGCCAGCTGCCTCGGGCGCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC