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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgagtcacgcatactaatgttgtcttatgaagttgtgagcctgattttgttctcttctatttag

Basic information

species Zea mays
transcript GRMZM2G023232_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 5
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgagtcacgcatactaatgttgtcttatgaagttgtgagcctgattttgt---tctcttctatttag
 ||||| |||||||| ||||||||||| |||||||||||||||||||| |||||||| ||||||||||| || |||||||| ||||||||||||||||||||||   ||||      |  | ||| | |   |||||  | ||| |   |  |  |   | ||||   || ||
TGAGAATGAGTATGAAATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAGGAGAAAAAGAATGCTGTCGAGGCTTATGTTTATGACATGCGTAACAAGgtatgccgagtttaattttgtgatgatat---atgaacatttgaacagtacctgatgagtttcttgcgttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 5
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgagtcacgcatactaatgttgtctta-tgaagttgtgagcctgattttgt-tctcttctatttag---------------------------------
||| || |||| ||| |||||| | |||||  | || |||||||||||||| || ||||| ||||| ||||| |||||||| ||||||||| | ||||||||   |   || |  | |  |  | || ||||| | | | | | |     | |     |  ||   || ||                                  
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggt---gttat-ctttttcttcttctcttactcagggtctaacatcaactacaaatgcctgtcatataattgttgatttttttttttccgttatcatttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 5
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgta-----tatt-------------------gagtca-----cgcatactaatgt-tgtcttatga-agttgtgagcctgattttgttctcttctatttag
|||||| |||| ||| |||||| | |||||  | || |||||||||||||| || ||||| || || ||||| |||||||| ||||||||| | ||||||||      |||                    | |||      | ||||| ||||  |||| ||| | | ||||     |  ||||  | |  ||  || ||
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAACGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggcgctatctttcttgttctcttacccagggtctaacatcacatacaaatgcctgtcatataataattgttgatttt-ttttcctgttatcatttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 6
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgagtcacgcatactaatgttgtcttatgaag----ttgtgagcctgattttgttctcttctatttag--------
|||||| |||| ||| |||||| | ||||| ||||| ||||| ||||||||||| ||||| ||||| || || |||||||| ||||||| | | ||||||||       | || |  |  |  |||| | | | || |    ||||     |  |     |   ||||  |||         
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTGATGGAGGAAACAAAGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattgccatg-gttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgta--------tattgagtcacgca--tactaatgttgtcttatgaagttgtgagcct--gattttgt--tctcttctatttag
 ||||| || | |||||||||| | ||||||||||| |||||||| || |||||   |||||||||||||||  ||||||| ||||| ||||| ||||| ||         ||||  |||       |   | | |     | | ||||||||||  |  | |  |    | |||| | || ||
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcattggcagtatgcatatgtaaagttgtgagtattgggtactaacgtgtcttgttttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgta---------tattgagtcacgca--tactaatgttgtcttatgaagttgtgagcct--gattttgt--tctcttctatttag
 ||||| || | |||||||||||| ||||||||||| |||||||| || |||||   |||||||||||||||  ||||||| ||||| ||||| ||||| ||          ||||  |||       |   | | |     | | ||||| ||||  |    |  ||   | |||| | || ||
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcattggcagtatgcatatgtaaagttttgagtattgagtactgacgtgtcttgttttcag

upper sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatat---tgagtcacgcatactaatgttgtcttatgaagttgtgagcctgattttgttctcttctatttag------------------
||| || |||| ||| |||||| | |||||  |||| |||||||||||||| || ||||||||||| || || || ||||| ||||||||| | |||||||||  |   |   ||       ||||    |  |||     ||   | |||     |  |    ||||   |                   
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag

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|32931686|gb|CF036498.1|CF036498
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGT
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGT
EST: gi|9952046|gb|BE638629.1|BE638629
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|89251181|gb|DY622967.1|DY622967
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|67032981|gb|CO461730.1|CO461730
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|18661122|gb|BM501223.1|BM501223
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|20803202|gb|BQ294252.1|BQ294252
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|67021901|gb|CO450650.1|CO450650
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|61119613|gb|DN560574.1|DN560574
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|67016035|gb|CO444784.1|CO444784
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGGAG-ACAAGGGAAGGTT
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTG-AGGACAAGG-AAGGTT
EST: gi|67025370|gb|CO454119.1|CO454119
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|32932457|gb|CF037269.1|CF037269
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|33094410|gb|CF054404.1|CF054404
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTAC
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTAC
EST: gi|211343665|gb|FL392042.1|FL392042
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
EST: gi|213174387|gb|FM187872.1|FM187872
EST:     AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAG                         CTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG
genomic: AGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTG

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: 879

AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 536

AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 664

AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgag ... ttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatattgagtcacgcatactaatgttgtcttatgaagttgtgagcctgattttgttctcttctatttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC