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

gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT

Basic information

species Zea mays
transcript GRMZM2G134176_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70140.1 (Oryza sativa), 3'ss of exon 2
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaacc--agcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                                                  |            |   ||     | |  ||   | |  |  |||   || ||||   |    |   |||   | | |   | ||||||||||| |||||||||||||||||| ||||||||||| |||||||| ||||||||||| ||||| || || ||||||||||||||||| |||||||| || || |||||||| 
-------------------------------------------------------------------------------------------------ttgtgacttatcagttgcgagtttgggattacttgaactttactggcgcttctttactgataactacaagtcttgattt--ctactccaatctatgttgaagGCACCCTAACATTAGCAGCCAAAACGGAGCAATCTGCTTGGACATACTGAAGGACCAATGGAGCCCAGCCCTTACATTGAAGACGGCACTGCTTTCCCTC

upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacc-tacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                         | ||| |    | ||||   | || || |||| || ||           | || || | |    ||||  || | | |     || ||||| | | |  |             |  |  ||||||||| ||||| ||||||||||||| |||||| |||||| |||| ||  |||| || |||||||||||||| || ||  |||||||||| || |||||  | 
-------------------------------------------------------------------------ttatgcattgcaaatataatatttaatgcattactatggc---------ataataatctgtttggttgattaatgtgtg---gatgttttttgcgtatgt-------------taaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G37620.3 (Glycine max), 3'ss of exon 3
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacc-tacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                         | ||| |    | ||||  || || || |||| || ||          || || |  | |     |||| |  ||  | |     |||||  ||| |  |             |  |  ||||||||| ||||| ||||||||||||| |||||| |||||| |||| ||  |||| || |||||||||||||| || ||  |||||||||| || |||||  | 
------------------------------------------------------------------------cttatgcattgcaaatatagcaattaatgcattactatgg---------gaaaatagtctgt----ttggttgattaatgtatggatttttgtgtgtatgt-------------taaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaac-cagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctcca-----atc-tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                                                       ||||  |  |||||  | || | |||         ||||  | ||  | |   |      ||    |    |  ||| | ||     |||  || || |||||||||||| |||||||| |||| ||||||||||||||||||||||||||| || ||||||||||| || |||||  ||||||| || ||||||||  | 
-------------------------------------------------------------------------------------------------------tccttcgtgcatga-taaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA

upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ07315 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttga--agGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                                                      |   |  || |  ||  | |||  ||| |    | |   || ||||||      ||  |||  ||| | |||  | ||     | || || |   ||||| || || |||||||||||||||||||| |||||| | |||||||| ||||| ||||||||||| || || ||| | ||||| || || ||||| || 
-----------------------------------------------------------------------------------------------------gtgagtgagagctcgagaaaagaggaacaaaaaatct--agtttttttt------ttcctttgatgctgatcttgtctcct---tttacttcgcccagGCATCCCAATATCAGCAGCCAAAATGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACCCTCAAGACGGCTCTACTTTCTCTC

upper sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27483 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttga--agGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                                                                                                      |   |  || || ||  | |||  ||| |    |  | | | ||||||      ||| |||  ||| | |||  | ||     | || ||||   ||||| || || |||||||||||||| ||||| |||||| | |||||||| ||||| ||||||||||| || || ||  | ||||| || || ||||| || 
-----------------------------------------------------------------------------------------------------gtgagtgagagcacgagaaaagaggaacaaaaaat-ctagttttttttt------tttctttgatgctgatcttgtctcct---tttactttgcccagGCATCCCAATATCAGCAGCCAAAACGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACTCTCAAGACGGCTCTACTTTCTCTC

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|211183786|gb|FL226958.1|FL226958
EST:     GTGGATATCCCTTTGAGCCTCCGAAGATGCAGTTCATCASCAAAGTATG                         GCACCCTAACATCAGCAGCCAAAATGGGAGCAATTTGCTTGGACATTCTGA
genomic: GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGG-AGCAATTTGCTTGGACATTCTGA
EST: gi|211011838|gb|FL066264.1|FL066264
EST:     GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATG                         GCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAA
genomic: GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAA

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: 192

GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 218

GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTGGATATCCCTTTGAGCCGCCGAAGATGCAGTTCATCACCAAAGTATGgtatgcaagt ... tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT
                            ctctgat  putative branch site (score: 163)
                                           tctatttt  putative PPT
     tttatccaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaaccagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctccaatctattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA