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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

Basic information

species Zea mays
transcript GRMZM2G142334_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactc---aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
||||||   | ||||||||||| ||||||  ||  ||||||| | |  ||||| |  | |   |||  |||||  ||  ||||| ||||| || ||     ||||||||| |||||||||||||||||||||| || ||||| || || |||||||| |||||||| || ||||||||  |||||||||||||||| |||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctgg--aacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
|| |  | | ||||||| | |||| ||||              |  ||||||||  |   |  |||  |  |  |    | |||   ||| | ||  |        ||| | |||||||||||||||||||| |||||||| || || ||||||||||||| |||||||||||||||  | ||  |||||||||| |||||
gttagat-tcccatgtttatataagtaat--------------gagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggc-----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatc-catgtgttactcaaaactgc-agTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
                   | |  |||| |||||     || ||   |||   |  |   | ||||  |||    | | ||| |      | ||  |  ||  ||| || | |||||||||||||||||||| ||||| ||||| || || || ||||||| |||||||||||||||  | |||||||||||||| |||||
-------------------gtttgataagtgatgaa---ttatg---aatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
|| |  | | |  |||| |||||| | ||  ||  |   ||     |      ||   | |  |   | |  |||       ||   | ||||  | || |   ||| | || ||||||||||||||||||||||| || || || || || ||||||| |||||||||||||||  |  ||||||||||||| |||||
gttagat-tcctgtgtttagataagtgatgaattatgaatttcattc------tactgctttgtcgagttataactggttatattt-tatgtt--tgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
|| |  | | |||||||  ||| |  |||  ||   |  |  |||   || ||              | |  |  ||  |||   | | | ||  |        ||| | |||||||||||||||||||| |||||||| || || ||||||||||||| |||||||||||||||  | ||  ||||||| || |||||
gttagat-tcccatgtttggatgagcaatgaat---ttctgctgctttatcaa--------------gttatagtaa--ctggctcttttttttttggc-----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
                         | |  | |  ||  |   |||   |  ||        | | || || ||   | |      |||| |||| |     ||||| |||| ||| |||||||||||||||| || || || ||||||||||||||||  ||||| |||||||| || |||||||| ||||| |||||
------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccgg--ttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
gtaatttc--ttccatgttaagataaataattgat-ggttctttgtgcacaatgaa--tagcacatatttttgctggaacaaacctgatccatgtg----------ttactcaaaactg---cagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
|| |||||  |||    | ||| |   |  ||  | ||| |||||     |||| |  ||        |||      ||  ||  ||| | || |           ||| | ||| ||    ||| | |||||||||||||||||||| || || ||||||||||||||||||||||  ||||| |||||| || |||| || ||||||||||||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttact---caaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
|| |  | | |  |  | ||| || |             ||   || ||  | |   ||||   | |       | ||  | | || | |||| ||   |    || ||||| |||||||||||||||||||| ||||| || || |||||||| |||||||  |||||||||||| |  | ||||| || ||||| |||||
gtgagct-tgctttcctcagaaaagt------------cttacacagaacaacttctacattactctctgcatgctaattttaccc-tctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
--gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagc--------acatatttttgctggaacaaacctgatccatgtgttactcaaaactg---cagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
  |  ||||  | | | | ||    |  |  | | ||     |  |||   |  |||             |||  ||      | ||   || |     |  |||||  | ||    ||||| || ||||| ||||||||||| ||||| || ||||| |||||||||||||  ||||| ||||||    |||| ||||||||||| |||||
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaatttcttccatgttaagataaataattgatggtt-ctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
   || |  | | |||||   | |     |  |  |  ||| ||   ||| ||   |||  |  |     || | | ||  | |    | |  ||        ||||| | |  |||||||| ||||||||||| ||||||||||| |||||||||||||  ||||| |||||  |  | ||||| ||||||||||||||
---atcttattcgtgttatttttatctggtattattggcttggtattcaa-gatccgcaggtgctgggaatgta-ctaatataagttgttttgtatc---gtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

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|67016408|gb|CO445157.1|CO445157
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
EST: gi|71417754|gb|DR804198.1|DR804198
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGT
EST: gi|6020391|gb|AW065319.1|AW065319
EST:     ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAG                         TTATGNGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAG
genomic: ATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAG

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), 47 (downstream exon)
Score: 82

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 44

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 82

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

CTTTGGGATGTTAAGATGAATTCTGGTCCTGTTGCAACATTCCAGGTTCATGAGTATCTAAGGCCTAAGgtaatttctt ... aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
                         acctgat  putative branch site (score: 86)
     acatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA