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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata...

Basic information

species Zea mays
transcript GRMZM2G451716_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA08G28860.1 (Glycine max), 5'ss of exon 6
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatg---ctctct----acttgtccatcactctc-----------tattatctg-ttgcatcatggtatatga-ctatatggtgactagtagttcctgaactctgctgcttatcgcata-----------------------------------------
||||||  ||||||| ||||| || ||||| ||||||||||||||||| |||||| | ||||| |||||| || | ||||| || ||||| || || || ||||     ||| |    |    | ||||||   |           | ||| ||| ||| | |||  ||||| | | |    |  | | | | ||  |||||     |  ||||                                               
AGCTCTCATTGCTCACTTCCAAAATTCAAGCTTGATGAATGAGGATAAGCGCTGCAGGCCTATCCTCTTCAACACCGATGGCCCTAATGCCGGTGACCAGgtataaatttcttttaagatccattcatcacgtacattacaggtattcttacctgcttgaaacataatatataatccaggcagccatttgaaatt--tgaacctctatttttattaagagatgaagctacaaaacggctactaactttgctaggaactcag

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatca--------ctctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata
  ||||  ||||||||||||||||||||||  |||||||||| || ||||| ||||| ||||| ||||||||  | ||||| || ||||| || ||||  |||          |||| | | |        || | ||||||||| | | || ||||   |||  | ||  |||  | || ||  |   |||||| |           
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttc-tggtg-gtgataaaat--tgatcaatatttttttgtctctgcag-----------

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA04G37810.1 (Glycine max), 5'ss of exon 12
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata
 |||||  |||||||||||||||| |||||  |||||||||| |||||||| ||||| ||||| ||||||||  | ||||| || ||||| || ||||  |||      ||  || |  |    |  ||||| ||  ||   | |    |    | |||      ||||      | ||  ||    |  | || |  | 
TGCTCTTATTGCTCATTTCCAGAATTCAAGCCTGATGAATGAAGATAAACGGTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcagcttgttctttagttgtaactattttccttttgctaactacaatgtattatggaactactatatcagcttgttcttcagttgtaattgtttt

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 13
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata-
||||||  |||| |||||||||||||||||||||||||| || || ||||| ||| | ||||| ||||||||| ||| |||||| ||||| || ||||| ||| |      |   |  ||          ||||       || |     |     |  |  || |  |     ||  | | |    |  | |    |   
AGCTCTTATTGCCCATTTCCAGAACTCAAGTTTGATGAACGAAGACAAACGTTGCAGGCCTATTCTCTTCCACACTGCTGGTCCAAATGCTGGTGATCAGgtaaggaagacaagggctcaattgatatccttattcaaactataacctctttctgttgca-agtaatcatatcatctggtagttatgtattcactatagcg

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctg--ttgcatcatg-gtatatgactatatggtgactagt---agttcctgaactctgctgcttatcgcata-------------------------------------------
||||||  |||| ||||||||||||||||| || ||||| || || ||||| ||||| ||||| ||||||||| |||||||||| ||||| || ||||| |||     |  |  |    |  | ||  | || | ||  |  ||| ||   |||     |   |     | |||   | ||| | |  ||    | |||  |  ||                                           
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 5'ss of exon 4
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctga--actctgctgcttatcgcata--
 |||||   |||||||||||| ||||| || |||||||||||||||||||  ||||||||||| || || ||  || ||||||| |||||||| ||||| ||| |   |||     |  |  |   ||| |  | ||||   || |  ||||  | |   |  |||||| || |   |||  |||    | | | ||    |  
TGCTCTTACTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACATTGCCGCCCTATTCTATTTCATACTAATGGTCCAAATGCAGGTGATCAGgtaggacatctgac-ataaagtatgttctctattttgttat-tctt--tatactaattggtaatgactattaatgtatgattacttgtatacctttccttgata

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctct-acttgtccatcactctctattat-ctgttgcatcatgg-tatatgactatatggtgac-tagtagttcctgaactctgctgcttatcgcata
 |||||  ||||||||||||| ||||| || |||||||||||||||||||| ||||||||||| || || ||  |||||||||| |||||||| ||||| ||| |   ||| || |         |||||||| |  ||||| |||  || | ||   || | |    |  |  |   | || |    |  ||  |||      
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta----

upper sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata----
 |||||  |||| |||||||||||||||||  |||||||||||||||| || || || || || ||||||||  |||||||||| |||||||| ||||| |||||      |  | | ||| |||    ||       |  |    | ||||    ||  |||  |  || |  ||| |||   ||  | | |  |||      
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatga---ggatctctacat-acttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa

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|78073984|gb|DV502418.1|DV502418
EST:     GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAA                         GAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
genomic: GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
EST: gi|5895966|gb|AW037212.1|AW037212
EST:     GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAA                         GAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
genomic: GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
EST: gi|5895962|gb|AW037208.1|AW037208
EST:     GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAA                         GAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
genomic: GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
EST: gi|166478607|gb|EG102617.1|EG102617
EST:     GCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAA                         GAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
genomic: GCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGG
EST: gi|91048864|gb|EB159282.1|EB159282
EST:     GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAA                         GAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCC
genomic: GCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCC

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: 268

AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGGATTTTGAGTTGGGAACAAAACCACCAGGACATTGTGTCTGATCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGGATTTTGAGTTGGGAACAAAACCACCAGGACATTGTGTCTGATCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGGATTTTGAGTTGGGAACAAAACCACCAGGACATTGTGTCTGATCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctc ... ctttccacagGAACCATTCCCTGTGGGATCAAATGTCCGTTCCAGGCCTGGAAGGTCCAGGATTTTGAGTTGGGAACAAAACCACCAGGACATTGTGTCTGATCATACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA