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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT

Basic information

species Zea mays
transcript GRMZM2G473001_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
|||||  ||| |||| |     |||||  |||    || | ||| |||     |||   | || || ||||||     ||  |||||   | | ||  |||      |     ||    |   |  ||||||     |||||     ||  | | | ||   |  | |         |||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||| ||||| || |||||||||||||||||
gtgagaaacatatctat-----tttgt--tgttggttcttagcactatgccttata---aataattacagcacaatgaatcctctttagatgttgtctttaaattactaccacttaggagataccatgtctgta---tgcac-----tctaaatttcaaatgaccttt--------acagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGATGTCTGCTTGCTTGCAAGAATGATGGCAGCAAACTTGTATTGCTCACAAATTGAGGATCTCATGTT

upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 5
----------------------gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcag-tatttgca-gcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtct--ctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                       | |  || |||    |   ||| |  ||  |  |  ||   | |||  ||       ||  ||||   |   ||  | |||  | ||    |  |||  || |||    |  |      |||| ||     ||   | | |   |  ||     ||| |   |||||||   |   | || ||| ||||| ||||| || || || |||||||||||||| || ||||| || |||||||||||  | ||  |||||| ||||||||| || |||||||||||
gtatctttcttttggctaagaaattaaagaaacaagcttttttatctaactctttgtgacaattccttactttttgcccccaaatattcatatagactaaatatctttttcagcttcagt--tttggacaccgcctcagagatgtggct-----tgtaatatacttattagtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACCAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATGTGTACTTCTCTCAGATAGAAGATCTCATGTT

upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                                                                         ||  ||      || ||||   |  |||  || | |  |  | ||| |       |   | |   |    | ||||  | | |    |||| |        ||||||| ||||||||||| || ||||| || || || ||||| |||||  | || |||||||||||  | |||||||||| ||| ||||| ||| |||| |||||
------------------------------------------------------------------------actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT

upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                                                                         ||  ||      | |||||   |  |||  || | |  |  | ||| ||      |   |||   |    | || |  | | |    |||| |        ||||||| ||||||||||| || || || || ||||| ||||| |||||  | || |||||||||||  | |||||||||| ||| ||||| |||||||| |||||
------------------------------------------------------------------------actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT

upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgc-agcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                                                               | ||| |  | |  |||       |  ||| |||| |     || || ||  || ||       |  | | |  |   ||||||   |||||       ||||| | |     |||||| || || || || || ||||| ||||| |||||||| || ||||| || |||||||||||  | || ||||||| ||||||||||||||||||||||||
---------------------------------------------------------------tgtgccaaaatcccttaaacataatccttcaagtgct----gaggtgttttctcgttcc-----taacagtgaatca-acctct-cactattt--gtctaatgtgtgt-----tgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT

upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
----------------------gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtct--ctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                       | | ||| |||    |   ||||   ||  |  |  ||   | |||  ||   |   ||  || | ||  |  ||| ||  | ||    |  |||  || |||   ||  |      |||| ||     ||   | | |   |  ||     ||| |   |||||||   |   | || ||| ||||| ||||| || || || ||||| |||||||| || ||||| || |||||||||||  | ||  |||||| ||||||||| ||||||||||||||
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaa-atgttca-tatgtat-atctttttcaacttcagt--ttgggacactgcctcagagatgtggct-----tgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT

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: 294

CGGGTTGATACTGCATTGAAGAACATTGGGATTAACGAGCGTGTTCCTTACAATGCACCTCTTATTCAATTCTCTTCTTGGATGGGGGGAGATCGTGATGgtgagtgaca ... acaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

CGGGTTGATACTGCATTGAAGAACATTGGGATTAACGAGCGTGTTCCTTACAATGCACCTCTTATTCAATTCTCTTCTTGGATGGGGGGAGATCGTGATGgtgagtgaca ... acaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 211

CGGGTTGATACTGCATTGAAGAACATTGGGATTAACGAGCGTGTTCCTTACAATGCACCTCTTATTCAATTCTCTTCTTGGATGGGGGGAGATCGTGATGgtgagtgaca ... acaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

CGGGTTGATACTGCATTGAAGAACATTGGGATTAACGAGCGTGTTCCTTACAATGCACCTCTTATTCAATTCTCTTCTTGGATGGGGGGAGATCGTGATGgtgagtgaca ... acaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
                           ttctaaa  putative branch site (score: 287)
                                        tctctac  putative PPT
                         tattctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT