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

gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC

Basic information

species Zea mays
transcript GRMZM2G117900_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 6
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgtt-acagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
                            || |   | |  ||||     | ||| ||  |   | || ||| | | || || | |      |||  |  | |   ||||| || || ||||||||||| || |||||||| |||||||| || ||||| |||||||||||||| || || |||||||||||||||||||||||||| |
--------------------------gtca-ctgttgcccatcatttcttatctagtagattatctcatctgtctttttgttt-atggagatttttttttctctgcagGGCACCATTGCTGAAGGTGCTCCAGTGGTGCCAATATCTGCTCAACTGAAGTACAACATTGATGTGATCTGTGAATACATTGTGAAGAAAATCCCCATTC

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 6
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagtgtct-tctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
                               | | |    || |  ||||      |       ||| ||| | | || || |     || |||  |   |  || |||| || |||||||||||||| || |||||||| |||||||| ||||| || || ||||||||||| || || |||||||||||||||||||||||||| |
---------------------------gttgctactgtccattattatcttgtagatgggtacatctgtctgtctatttgtttatgggttattttatttctctat-agGGTACCATAGCTGAAGGTGCTCCGGTGGTGCCAATATCTGCTCAGCTTAAGTATAACATTGATGTGATATGTGAATACATTGTGAAGAAAATCCCCATTC

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 6
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
        | ||| |  ||||   |     ||   |||  |     ||  || ||       |  |||   |  |    | |  ||| | |||  | |||||  ||||||||  | ||||| |||||||| || || ||||| || || ||| |||| || || ||||||||| | |||||||| ||||||||||| ||||| ||||
-------gtaagttt-tctttaaagagatttcttctacacaagtgaattcctttt----tgataacttaaatgac--aatttccccccttttttgtgatttg-ccagGGAACTGTTGCTGATGGTGCACCAGTAGTACCTATTTCAGCACAGTTGAAGTATAATATTGATGTTGTGTGCGAATATATTGTGAAGAAGATCCCAATCC

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagt---gtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATA--GCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
|| |    |   | | |  ||  ||  |  |   |   || |||     || |||| |  ||    || ||      ||||||   |   ||  || | |||    |    ||||| |   ||||| | ||| ||  | || ||| | || || || ||||||||||||||||||||  | ||||| |||||||| ||||| ||||| ||||
gttaggttttcttat-ctcttaaggatctgttgtagcattctcatttcgtcacttggttaagctaagtattgaagaacttggttctaaaatttctttcacatcctgttgcagAACACTGTTGCTGATGCTGCTCCGATCGTCCCTGTCTCAGCACAACTGAAATACAACATTGATGTGGTGTGCGAGTACATTGTCAAGAAGATCCCAATCC

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|148932915|gb|EE285716.2|EE285716
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTG
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTG
EST: gi|32840734|gb|CD980415.1|CD980415
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32942799|gb|CF047618.1|CF047618
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32932475|gb|CF037287.1|CF037287
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCT
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCT
EST: gi|32935513|gb|CF040325.1|CF040325
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCT
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCT
EST: gi|67038206|gb|CO464536.1|CO464536
EST:     GAAAGTGCAGCAATGAAATCA-CATGAAAGCA-TCCAAAAATTCATC-AG                         GGGACAATAGCTGAAGG-GCACCTGTGGTGC-TATATCTGCCCAGCCTGAA
genomic: -AAAGTGCAGCAATGAA-TCAACATGAA-GCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGC-TGAA
EST: gi|32944740|gb|CF049559.1|CF049559
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATC
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATC
EST: gi|32940834|gb|CF045653.1|CF045653
EST:     GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|71449155|gb|DR830205.1|DR830205
EST:     GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCTAG                         GAAACA-TAGCTGAAGGTGCACCTGTGGTGCCTATATCTG
genomic: GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCC-AGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTG
EST: gi|32934531|gb|CF039343.1|CF039343
EST:     TGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: TGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32945952|gb|CF050771.1|CF050771
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCGCCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32945454|gb|CF050273.1|CF050273
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32841334|gb|CD981015.1|CD981015
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|33095600|gb|CF055594.1|CF055594
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32941656|gb|CF046475.1|CF046475
EST:     GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: GGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
EST: gi|32943977|gb|CF048796.1|CF048796
EST:     AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAG                         GGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA
genomic: AGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAA

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: 598

CATGCGCCTTCAACATATCATCATTCTGCAGAACAAGATTGATCTTATCCAGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 479

CATGCGCCTTCAACATATCATCATTCTGCAGAACAAGATTGATCTTATCCAGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 515

CATGCGCCTTCAACATATCATCATTCTGCAGAACAAGATTGATCTTATCCAGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 442

CATGCGCCTTCAACATATCATCATTCTGCAGAACAAGATTGATCTTATCCAGGAAAGTGCAGCAATGAATCAACATGAAGCAATCCAAAAATTCATCCAGgtcaatactc ... atttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttacagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC
                          gtctgac  putative branch site (score: 442)
                                cccttctttgctcatt  CT-rich tract
                                             atttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatactcagtgtgcctttgcggcaccatccaatacttatcaccatctctcttgttacagtgtcttctctttcttggtctgacccttctttgctcatttgatcagGGAACAATAGCTGAAGGTGCACCTGTGGTGCCTATATCTGCCCAGCTGAAATACAACATTGATGTTATTTGCGAATACATTGTGAAGAAAATCCCCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA