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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA

Basic information

species Zea mays
transcript GRMZM2G098714_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 9
gtataatcgtc-aatatccactgaacgatgatattatttat-atcttgaattga--aaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
||| |||| |  ||| |       |  |||  ||| ||  | || || | || |  |  | | |  | |||       || || || ||   ||       ||  ||||||||||| ||||||||| || |||||   || ||||  |||||||||||||| | |||||||||||| ||||||||||||||||||||||||||||||||  
gtaaaatcttggaatctttgaaagaaaatggaattgttcttgatgtttagtttattagcactttctagttgtgattgtcctaaatttacttgtta------tgttttgcagCCTGTGTTCTTCAGTCTGAATGCCTATATTAGCCTTATCAAGCCTGACCAAACCATGTGGTACCGAGCTTGCAAGACCTGCAACAAGAAGGTGACTGAGG

upper sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
                     | ||  | | |  | || || | |  ||| | | || | |||     ||||      ||||     | |  | | |   |||||||||||| ||||||||       ||   |||||||  ||||||||| ||||| |  |||||||||||||||||||||||||| |||||||| || |||||| 
---------------------gtact-tcaaaacacttttaacat--attaagatatggaaaa----aagaaaagttgatttatgagtctcgtatat-atattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG

upper sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
gtataatcgtcaatatccactgaacga--tgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgaccctttta--tttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
   ||||  | | | ||    |||  |  | | || ||  |  |  |       ||| || | | ||   || |    || |||      | |    ||||     | ||||||   || || ||  |    ||   |||||||  |||||||||||| || |  ||||||||||| ||||| ||||| ||||||||||| || || ||  
--gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

upper sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0587g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattga---aaaattgtaaatttggagaacccccaatttgaccctttta--tttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
   ||||  | | | || | | ||  |   ||  ||    | | ||   | |   ||| || | | ||   || |    || |||      | |    ||||     | ||||||   || || ||  |    ||   |||||||  |||||||||||| || |  ||||||||||| ||||| ||||| ||||||||||| || || |   
--gtaataattactgtc-attaaaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGGTG

upper sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 9
gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattga---aaaattgtaaatttggagaacccccaatttgaccctttta--tttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
   ||||  | | | || | | ||  |   ||  ||    |   ||   | |   ||| || | | ||   |  |    || |||      | |    ||||  |  | ||||||   || || ||  |    ||   |||||||  |||||||||||| || |  ||||||||||| ||||| ||||| ||||||||||| || || ||  
--gtaataattactgtc-attaaaataacttaacatgaccaaactggtcttagccaaagttttgagttaaaaccatattcagttttgataatgtgggcttgtctctgtacagCCTTCCTTTTTTAGCATCAGGGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG

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|211343900|gb|FL063189.1|FL063189
EST:     GTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAG                         CCTGTTTTCTTTAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
genomic: GTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
EST: gi|60348547|gb|DN215520.1|DN215520
EST:     GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAG                         CCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
genomic: GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
EST: gi|32938350|gb|CF043169.1|CF043169
EST:     GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAG                         CCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
genomic: GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
EST: gi|211343908|gb|FL063197.1|FL063197
EST:     CTGCCATGGGCCAGGAAAAG                         CCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
genomic: CTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
EST: gi|211341514|gb|FL063180.1|FL063180
EST:     GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAG                         CCTGTTTTCTTTAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG
genomic: GAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 158

AGAAATGGGTGCCGCACGGGCCGGTGGCTTCAAGTCCACGTATTCTGATAGAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 25

AGAAATGGGTGCCGCACGGGCCGGTGGCTTCAAGTCCACGTATTCTGATAGAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 39

AGAAATGGGTGCCGCACGGGCCGGTGGCTTCAAGTCCACGTATTCTGATAGAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 5

AGAAATGGGTGCCGCACGGGCCGGTGGCTTCAAGTCCACGTATTCTGATAGAGTTTTTCTGTCTCACATTACTAGTGATCCTGCCATGGGCCAGGAAAAGgtataatcgt ... tgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
                          atttgac  putative branch site (score: 5)
                                cccttttatttgtt  CT-rich tract
                                   ttttatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG