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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt...

Basic information

species Zea mays
transcript GRMZM2G181151_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa-ggacttatgaatttgtgatcaacattcatttaccattt--------tatttctcccaagagtgccataatcggtt-ctgcattgttttagatgcat-att---------------------------------------------------------------------
||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||||| || |   ||||| |||| || ||||  | |   ||||   ||          || |||| | |         |  |   || ||| || ||| || |||||| |||                                                                     
GTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgta-cctacaaggacttatgaatttgtgatcaacattcatttaccatt--ttatttctcccaa--gagtgccataatcggttctgcattgttttagatgcatatt
 ||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| ||||| || || |||||  | || || ||||| || ||| ||||| ||    |  | |||  ||| ||  | |  || |  |  | |||   |||  | |   |   || |||    |       ||  |        |    |   
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaatta-aaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtg-gtgaccaagaaaaggt---

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt-
|||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| ||||| || || |||||  | || |||||||| || |||||||||      || ||   |       || ||     |     |    ||| ||  |  |  |  | ||  | |   ||||   |  |||||  |   || | 
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttatt-cccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt-----
 ||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| || || || || |||||  | || |||||||| || |||||||||      || ||     | | ||  |      ||   || | ||||  ||  |    |     |   | |   ||||   |  ||||   |   ||||     
-TTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGGtagtctttagaacc----agtatgcaaatgctcttttattcctatttctttgttgtttacttgccttcatttccttctttgtaattttgtctatgtatttgaga

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtac------ctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagt--gccataatcggttctgcattgttttagatgcatatt
|||||| |||||||| ||||||||||| |||||||| |||||||| || ||||||||||| || || || |||||  | || || ||||| ||||| ||||||       || | |   || ||     | | ||  |  ||  |  |  ||||   |  | |  ||  |    || | |      | | || ||  |   |      
GTTTGCAGCTATGGGTGTGAACATGGAGACAGCTCAGTTCTTCAAGCGAGATTTTGAAGAAAATGGATCAATGGAGAGAGTTACTCTTTTCCTGAACCTGgtaaatttgacttctatagctgattgccatatcatggagttttttcaagtatttagatgtttcttagctttaaacagatttaaccttcctttattccaacag------

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgta-cctacaaggacttatga--atttgtgatcaacattcatttaccattttatttctcccaagagtgccata----atcggttctgcattgttttagatgcatatt------------
 ||||| |||||||| || |||||||| |||||||| || ||||| |||||||||||||| || || || |||||| |||| |||||||| |||||  |||||   ||| ||    ||  |  | | || ||    || |  || | || ||| ||||   |  | |  ||||    ||| ||   | ||||   |   |    |||            
TTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGATGGAAAGGGTTACCCTTTTCCTGAACTTGgtaatttactagttactagtactactagtaatttctatgc--ttccaatcttacttcttgtagtactatcatattatatcagtgaggaattgaccttattatgcattccactcgaacag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctac-aaggacttatgaatttgtgatcaacat-tcatttaccattttatttctc---ccaagagtgccataatcggttctgcattgttttagatgcatatt--------------------
 ||||||||||||||||| |||||||||||||| ||||| || || ||||||||||| || || || ||||||||  | || |||||||| || ||  ||||| | |  ||  | |||     || |  | |  || |  ||||  ||  | | ||||    ||     |    |    ||| |   |  ||| | ||   || |                    
CTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCATGGAGAGAGTGACCCTTTTCCTAAACTTGgtatcaattaataatttaatctcttatcctaattatgttgtttaggatgatctctctcatttcatttaggtggaagggtgttttttttcttttaatatttgtaatgatgtggctcttttgcacag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacct-acaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt-----
 ||||| ||||||||||| |||||||| ||||||   ||||||||||||||||| || || ||||| ||||||||  | || || |||||||| ||| ||||| || ||    | |  | |  || || | ||||        | |   ||| |   ||  |  ||   |     |||| | | |   |   || | | ||     
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacg-----gcaaagatatcttcaccgtggttgt-gttcctagttcagaactagctcttattccttttccctg

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggact-tatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt----------------------------------------------------------------------------------------------------
 || || ||||||||||||||||||||||| ||    ||||||||||| ||||||||||| || || ||||||||  | || || |||||||| ||| |||||  ||||    |  | |   ||| |  || |  ||||       |||   || |     ||    |||   | |||     | ||  | || |  |  |                                                                                                    
TTTCGCCGCTATGGGAGTGAACATGGAAACTGCCACTTTCTTCAAACGCGATTTTGAAGAAAATGGATCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcat--ccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcag

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|30307204|gb|CD001877.1|CD001877
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32908718|gb|CF013531.1|CF013531
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCC
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCC
EST: gi|60352515|gb|DN219488.1|DN219488
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32945519|gb|CF050338.1|CF050338
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATAAG                         GATAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|31360502|gb|CD444859.1|CD444859
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32933270|gb|CF038082.1|CF038082
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|60394888|gb|DN227757.1|DN227757
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|67015926|gb|CO444675.1|CO444675
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|67028686|gb|CO457435.1|CO457435
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|26557381|gb|CA829616.1|CA829616
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32944897|gb|CF049716.1|CF049716
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32846162|gb|CD985843.1|CD985843
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32933397|gb|CF038209.1|CF038209
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAAAC
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAA-C
EST: gi|32942779|gb|CF047598.1|CF047598
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GTTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
EST: gi|32931129|gb|CF035941.1|CF035941
EST:     ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTG                         GCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA
genomic: ATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACA

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: 1016

GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1021

GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 781

GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1356

GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaa ... cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA