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

...gtttggtcacaagcgattgatgcggctgtttgactttattttcatcgtggattccatgactctggttgtaataacatttgtctttatatttcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG

Basic information

species Zea mays
transcript GRMZM2G165195_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 5
gtttggtcacaagcgattg-atgcggctgtttgactttattttcatcgtggattccatgactctggttgt-aataacatttgtctttatatttct--tttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG--
       | | ||| |||  ||  | |      |   | || | || |   |||  || | |    || | || | || || | ||| | |||||  |||| |||||||||||||||| ||||| |||||||| || |||||||| || ||||||||||| ||||||||||||||||||||||| |||  |||    |  |  |  
----aaactccagcaattttatctgacaaaaatatccttttgttatggaccattttattatttaaattattaagagcaattatgtttctttttctattttgtagCGACAAGCTGTTGCTGAGGGCGCTGATGATGATGAGGAAGATCTGGAAGAGATCAGAGCACGGCTTGCTAAAGTGAGGTCATAA--CATTCTAACTTTGGGA
















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|211495219|gb|FL000399.1|FL000399
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAG                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|76010550|gb|DT937720.1|DT937720
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|91052905|gb|EB163323.1|EB163323
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|91054729|gb|EB165147.1|EB165147
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGC
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGC
EST: gi|211298305|gb|FL473376.1|FL473376
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|13558970|gb|BG550325.1|BG550325
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|148991100|gb|EE032548.2|EE032548
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|71765371|gb|DR963308.1|DR963308
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|32867970|gb|CF007652.1|CF007652
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAG                         CGACAAGCTGTTGCTGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|71765372|gb|DR963309.1|DR963309
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|78074982|gb|DV503416.1|DV503416
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|76281952|gb|DV021520.1|DV021520
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|32867969|gb|CF007651.1|CF007651
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAG                         CGACAAGCTGTTGCTGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|76010551|gb|DT937721.1|DT937721
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|211095886|gb|FL432128.1|FL432128
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
EST: gi|76933730|gb|DV173563.1|DV173563
EST:     CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAA                         CGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG
genomic: CCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAG

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: 202

GGTTCTTGCTTCAGTAGCTGGGGAGACTGCCTCCCAGCTACCAGATGCTGCCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 192

GGTTCTTGCTTCAGTAGCTGGGGAGACTGCCTCCCAGCTACCAGATGCTGCCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GGTTCTTGCTTCAGTAGCTGGGGAGACTGCCTCCCAGCTACCAGATGCTGCCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 214

GGTTCTTGCTTCAGTAGCTGGGGAGACTGCCTCCCAGCTACCAGATGCTGCCAGAACACAGAAGATACATGAGGCTTCAACAAGCAGGGTTCCAGAAGAAgtaactaact ... tcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtggattccatgactctggttgtaataacatttgtctttatatttcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG
                       taataac  putative branch site (score: 214)
                                   tctttatatttctttt  putative PPT
                       taataacatttgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtcacaagcgattgatgcggctgtttgactttattttcatcgtggattccatgactctggttgtaataacatttgtctttatatttcttttgcagCGACAAGCTGTTGCAGAGGGTGCTGATGACGACGAGGAAGACCTAGAAGAGATCAGGGCACGGCTTGCTAAAGTGAGGTCGTAAATCATATACATATCTG

- - - -cacaagc
- - - - - - - - - - -gcggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca