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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag

Basic information

species Zea mays
transcript GRMZM2G103070_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g09740.2 (Oryza sativa), 5'ss of exon 14
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaa-tcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag
| |||||||| ||||| || |||||||| |||||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||   ||||| || ||| ||| ||| ||| |  | |   ||  || | |      ||||  ||||  ||||   |||||||
CGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTGTGATGTTAGAGCTATTGACAGGGCGGAAACCACTAGACAGgtatgct-tctagtttatattcaaatcccggtgcattgcgttttataaattg-----aaaatgaccttctgatggatattgcag

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA09G00970.1 (Glycine max), 5'ss of exon 14
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgt--tgaaatagcctttggatgatcattgcag-----------------------------------
| ||||||||| | |||||  | || |||||||| || ||||| ||||| ||||| ||||| ||| | || |||||||| || ||||||||||| |||||||  |    | | | |  ||  ||      |    | || |    || || || |  |  | ||   | |   |  ||  |   |                                   
CTGAGTTTGCATTATCTGGAGTATACACTGTAAAAAGTGATGTTTACAGCTTTGGGGTGGTTATGCTGGAACTATTGACTGGTCGGAAGCCACTTGACAGgtgagcctaccatacttgatgtaaaga-aatcatgtccatcacttaaatgtttatccttcattattatctttcttttctgtatggcttcttacattcatttgtaatttttgcaagtttag

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA15G11820.1 (Glycine max), 5'ss of exon 14
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatg--tgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag-----------------------------------
| ||||||||| | || ||  | || |||||||| || ||||| ||||| ||||| ||||| ||| | || |||||||| || ||||||||||| |||||||  |  |    || ||  | |  | |  |  |   | ||| |||  | ||      |  | ||   | |   |  ||  |   |                                   
CTGAGTTTGCATTATCAGGAGTATACACTGTAAAAAGTGATGTTTACAGCTTTGGGGTGGTTATGCTGGAACTATTGACTGGTCGGAAGCCACTTGACAGgtgagcctatcgtacatgatgtaaagtaatcatgtccatca-ctttaatgtttacccttcattattatctttcttttctgtatggcttcttacattcatttgtaatttttgcaagtttag

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT4G22130.2 (Arabidopsis thaliana), 5'ss of exon 9
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagatt---gtatccaatcctggttcgcttcagcttcgaagtggttgttgaaat-agcctttggatgatcattgcag---------------
||||||||||| |||| || ||||| || || || || |||||||||| ||||||||| || ||| | ||||| || || || |||||||| || ||||||| | |  ||    ||   ||| |||||  ||        |   |  ||         |||  | ||  |    |||   | ||                  
CAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAGTCATGCTTGAGCTCTTAACTGGTCGGAAGCCTCTTGACAGgtttcttttcatatttttagtagccaatgttgagcaatagccaatgtgagcaaaagcctgatttgagtttccttatgtaaaatgtgctttgtgtatgtgtag

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ07060 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaat---agcctttggatgatcattgcag
| |||||||| ||||||||| | || ||||| ||||||||||| ||||| ||||||||||| ||| | |||||  | || ||  | ||  | |||||||||||    |||| ||   | | | ||||  |   | || |  |   ||||        || |   | | |   |             
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaa--atcttgaagttcttccatccaaga--gttttatgt---aagtaagctccaaacttgaaacttccag-------------

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ37538 (Selaginella moellendorffii), 5'ss of exon 13
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag
| |||||||||||||||||  ||||||| || || |||||||| ||||||||||||||||| ||| | |||||| |||||||||| ||||| || |||||||| |   ||    || |      |  |   |  | | ||||   ||| |||  |  |   ||                    
CTGAGTTTGCAATGTCTGGTGTTTATACCGTTAAAAGCGATGTGTACAGTTTTGGAGTGGTGATGCTGGAGCTACTGACAGGGCGTAAGCCTCTGGACAGgtaaggtttcctagtt-ttcaaggttatatgttccattagct--aaagaggtgttctattcag--------------------

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ34030 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag
| |||||||||||||||||  ||||||| || || |||||||| ||||||||||||||||| ||| | |||||| |||||||||| ||||| || |||||||| |   ||    || |      |  |   |  | | ||||   ||| |||  |  |   ||                    
CGGAGTTTGCAATGTCTGGTGTTTATACCGTTAAAAGCGATGTGTACAGTTTTGGAGTGGTGATGCTGGAGCTACTGACAGGGCGTAAGCCTCTGGACAGgtaaggtttcctagtt-ttcaaggttatatgttccattagct--aaagaggtgttctattcag--------------------

upper sequence: GRMZM2G103070_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ18843 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgta-tccaatcctggttcgcttcagcttcgaagtggttgttgaaat---agcctttggatgatcattgcag
| |||||||| ||||||||| | || ||||| ||||||||||| ||||| ||||||||||| ||| | |||||  | || ||  | ||  | |||||||||||   | |  |    ||  | | ||||  |   | || |  |   ||||        || |   | | |   |             
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaaagcttgaagaagttcttccatccaaga--gttttatgt---aagtaagctccaaacttgaaacttccag-------------

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|60397323|gb|DN230139.1|DN230139
EST:     TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAG                         TTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
genomic: TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
EST: gi|71433499|gb|DR814549.1|DR814549
EST:     TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAG                         TTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
genomic: TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
EST: gi|60347761|gb|DN214734.1|DN214734
EST:     TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAG                         TTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
genomic: TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
EST: gi|32935389|gb|CF040201.1|CF040201
EST:     TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAG                         TTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT
genomic: TTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACT

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: 123

CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 45

CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 47

CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 65

CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatc ... atcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGGTAATGTTAGAGCTATTGACAGGGCGGAAGCCACTAGACAGgtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT