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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtatattattgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag

Basic information

species Zea mays
transcript GRMZM2G167999_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtatattattgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag
||| ||| |||||||||||||||||||||||||||| || ||||| ||||||||||||||| | ||| ||||||| || ||||||||||||||||| || |||||| || ||        |  | | ||| ||| |  ||    |||    || ||||| ||  ||| || | ||  |  |||
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtt--------tcaaatgttgcataattgcttcttttctgaattctgaaccttcctgt-tttcttggatggcag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G30050.1 (Glycine max), 5'ss of exon 8
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtat-----attat--------tgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag-------------------------
 || ||||| ||||||||||| || ||||| |||||| ||||||| |||||||||||| |  ||||| ||||||| || |||||||| |||||    |||||||||  | || |    |  ||     |||||        |||||    |   |   || | ||||||     ||| ||    | |||||| | |                         
ACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTATAGTGGTGGTAGAGACTCTTCTgtgagtgcagtttttcgataaatttttaattatcatgactttgaatttatatgatgtctccttgttttgcttaatta-gtgaagcttgtgttactgattcgtaattcttttatttttgtag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G40360.1 (Glycine max), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatct--tgtgtatattattgaatagtcactgtacttcgtcgttttgaactt---ttatgtattccctgtgttccag---------------------------------------------------
| | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || ||||| || |||||    || ||||||   |   |||  |   | ||  ||  ||   |   | |  |    | | ||||| ||   | |  ||    ||   || |                                                     
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcgaccttctattaaatttaacatcaaactatttttttgttattacatcttgaatttatgtcacataacatctccttttcttgtttaacttgtgaacctcatcttctaatgttgtattcttttataccctaag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G40440.4 (Glycine max), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgta--tattattgaatagtcactgtacttcgt-----cgttttgaacttttatg----tattccctgtgttccag--------------------------------------------------
| | ||||| ||||||||||| || ||||| ||||||||||||||||| || ||||| || |||||| ||||||| || ||||| || |||||    || |||||| |||   |||  |  |  ||  ||  ||   |   | |   |  |     | | |||||||| | ||     ||  |   | |||| |                                                  
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTCGCCAGCACCCCAGCATTTAGTCATGTTTATAGTGGCGGGAGAGACTTTTCAgtgagtgaaaccttctattaaaattaacatcaaactatatttttttattattactacatcttgaacttatgtgacatcatatctccttttcctgtttaacttgtgaacctcatcttctaatgccgtattcttttataccttaag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G43070.1 (Glycine max), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgta--tattattgaatagtcactg-----tacttcgtcgttttgaacttttatgtattc----cctgtgttccag--------------------------------------------------
| | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || ||||| || |||||    || |||||| |||   |||  || |  ||  ||  ||   |   |      || |    | | ||||  || | || | ||    |   | |||| |                                                  
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgaaaccttctactgaaattaacatcaaactattttttattattattattacatcttgagtttatgtgaaatcacatctccttttcctgtttaacttgtgaacctcgtcttctaatgtcatattcttttatgccttaag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G42990.1 (Glycine max), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatct--tgtgtatattattgaatagtcactgtacttcgtcg--ttttgaactt-ttatgt-attccctgtgttccag--------------------------------------------------
  | ||||| ||||||||||| || ||||| |||||||||||||||||||| ||||| ||  ||||| ||||||| || ||||| || |||||    || ||||||  ||   |||  |   | ||  ||  ||       | |   || ||   | ||||| || | |  | |   |   | |||  |                                                  
AAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcaaccttctattaaatttaacatcaaactaattttttttatcatcacatcttgaatttgtcacattacatctccttttcttgtttaactagtgaacctcgtattctaatgttgtattcttttataccctaag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaatt--atcttgtgtatattattgaatagt---cactgtacttcgtcgttttgaacttttatgtattccctgtgttccag----
||| ||| ||||| | ||||| |||||||| |||||||||||||| |||||| |||  ||  ||||| ||||||| || || ||||||||||| |||| |||||||  |     | ||||| | | |  |||  |      ||  |||   | || ||||  | ||| || |||    | |||| | |    
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtatattattgaat--agtcactgtacttcgtcgttttgaacttttat-gtattccctgtgttccag-------------------------------------------------------------------------------------------------------------
| | || || ||||| ||||| |||||||| |||||||| ||||||||||||||||| ||  ||||| | ||||| || |||||||| || || |  || ||||||  | || |||     |  | |   |||  |   | |   || | || || | |  ||||    |  |   | |  |  ||                                                                                                             
GAGATGCGTGCATTCCTATGCCGTGCATACAGATTCTGTCTGGGCACTTGCAAGCACCCCAACATTTAGCCATGTTTATAGTGGTGGGAGGGACCTTTCCgtgagtacagttttctcccagaactcaaccaatgcaaatattcccctgcctctttcttatgttttgccattatttttttcctttagcatatgatgttttctcccttttttctttctctatctctctctctctctcttttctgatctttttctgcaatactcatcctttgatgcccaattctgtttatactctcag

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: PP1S69_10V6.1 (Physcomitrella patens), 5'ss of exon 9
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagtt-------aaattatcttgtgtatattattgaat--agtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag--------
 || ||  ||||||||||||| || ||||| |||||||| ||||| ||||||||||| ||| | ||  |||| || || ||||| ||  | ||    |||||  |||       |      |||  |||| |    || |  |||   |  |  | |   |  | |  ||||  | ||  ||    | | |         
ACGCTGCATTCATTCTTATGCAGTTCATACAGATTCTGTCTGGGCTCTTGCAAGCACGCCTTCCTTCAGTCACGTGTATAGTGGCGGTCGTGACTTTTCTgtacgttcctacaaaggcctcctttagtatttcgcagatttcagtgctttcaaattgcgatcattacttttttagcatcaccaccttacaaatgcccatg

upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
lower sequence: PP1S28_153V6.1 (Physcomitrella patens), 5'ss of exon 7
---GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagtta---aattatcttgtgtatattattgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag----------------
    |||||  ||||||||||||| || || | ||||||||||||||| ||||||||||| ||  ||||  ||||||| || |||||| |    ||    ||||| ||||    ||    ||  |  ||  | |||  |  |  | || ||  ||     | ||   | |    || ||  | ||  |                 
ACAACGTTGCATTCATTCTTATGCGGTTCACATTGATTCTGTTTGGGCCCTTGCAAGCACGCCATCATTCAGTCATGTGTATAGTGGTCGC---GACTTCTCTgtaagttctttaaaggactacttaatgcttttggctgttggcagttct--gttcacgttaatcatcacaatttacccatcttgtaaatatttgataattaca

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|71433407|gb|DR814457.1|DR814457
EST:     CAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCT                         GTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAAT
genomic: CAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaa ... tgtgttccagGTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAAT




















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), 48 (downstream exon)
Score: 106

GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaa ... tgtgttccagGTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAATGAATACCCTGTTCTACAGTTGTCTCTGCAAGATGACACAATATGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaa ... tgtgttccagGTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAATGAATACCCTGTTCTACAGTTGTCTCTGCAAGATGACACAATATGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaa ... tgtgttccagGTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAATGAATACCCTGTTCTACAGTTGTCTCTGCAAGATGACACAATATGGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaa ... tgtgttccagGTATACCTAACAGATTTGTCCACAAGAGAGAGTCTTTTACTCTGCACAAATGAATACCCTGTTCTACAGTTGTCTCTGCAAGATGACACAATATGGGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtatattattgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA