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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC

Basic information

species Zea mays
transcript GRMZM2G032505_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------------gggaggtccctttgttccatcagtcttatataagaaatga-ataatgccgtgttgctcatctgttacatg------tatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC
                                                                                  ||  |  |||||  |     || |  || |   |||  | | | || |    ||  ||  || |||        ||  |||  ||  ||| | ||||||| ||||||||||||||||| |||||||||||  |||| |||||||| ||||| |||||||| |||||||| ||||| || || ||||| ||||||||||| ||||
gtacattgcttaataaatgttgaaagttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgct--tcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatagATTCAAGAGCTTGTGGAGGCAATTGTTTTGCCAATGACACACAAAGATCGGTTCCAAAAGTTGGGCATTCGCCCCCCCAAAGGAGTTCTTTTGTATGGAC

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 4
---gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC
    |  | |  || |  |   ||| | ||   | ||   | | ||   | | ||     || || |    ||  || |    |||| ||| ||| ||   |||| ||||| ||||| || || |||||  |||| ||||| |||||||| | |||| | ||||||||||| ||||| |||||||| || || ||||| || |
gctagttgatgactctcctgtttca-tgtttccttagtttttagtatctctg-gtacaatatttgatgttggtgactctcctgtttt-tgtaattaaac--agATACAAGAACTTGTTGAAGCCATTGTGTTGCCAATGACTCATAAAGAGCAGTTCGAAAAGTTGGGTATCCGTCCACCAAAAGGTGTACTCTTGTATGGTC

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 4
gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttaca-tgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC
                     |   |||||  |       |   ||| || |||    |   |   | || | ||  |  | ||||| || | |||   |||| ||||||||||||||||||||||| || |||||||| || || || || ||  ||||| ||||| ||||||| ||||| || || || ||||| || |
-------------------gtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagtgaaactaattgagtttatttc-tggaac--agATCCAAGAGCTTGTAGAGGCAATTGTGCTTCCCATGACGCACAAGGAACGTTTTGAGAAGCTGGGTGTTCGTCCACCAAAGGGAGTGCTCTTGTATGGTC

upper sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 4
gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC
 | | ||  |  | ||       | ||||    ||| ||  |  |||  |||      | || ||| |  | ||    || ||      | | |    |||| |||||  | || |||||||||||  |||||||||||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| ||||
-gcaagtttcaattttgtgcatattttatg---gaagtggttgttgct-tgtccgatttttgatactttcaacta--aaacttgcctctaattacaacagATCCAAGAATTAGTTGAGGCAATTGTTTTGCCCATGACACATAAGGAGCGGTTTCAGAAATTAGGTATTCGCCCACCTAAAGGAGTGCTTTTGTATGGAC

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|149101527|gb|EE187650.2|EE187650
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|148951330|gb|EC897040.2|EC897040
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|22473221|gb|BU037701.1|BU037701
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGC
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGC
EST: gi|149109720|gb|EE293507.2|EE293507
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149085416|gb|EE174922.2|EE174922
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|22473395|gb|BU037875.1|BU037875
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTT
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTT
EST: gi|22133556|gb|BQ833772.1|BQ833772
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|148979721|gb|EE026794.2|EE026794
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|21809844|gb|BQ668162.1|BQ668162
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|32823651|gb|CD963373.1|CD963373
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149096589|gb|EE182348.2|EE182348
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|74241694|gb|DT649608.1|DT649608
EST:     ATGANAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|116820064|gb|EC863249.1|EC863249
EST:     ATGAAAAGCCCACTGAAGATTATAATGGCATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|60346168|gb|DN213141.1|DN213141
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAAAGGCAATTGTACTGCCCATGACACATAAAGACCG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCG
EST: gi|149062853|gb|EE157572.2|EE157572
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149077127|gb|EE165787.2|EE165787
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|78179300|gb|DV549673.1|DV549673
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
EST: gi|149100563|gb|EE186648.2|EE186648
EST:     ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAG                         ATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG
genomic: ATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGG

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: 276

AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 249

AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnn ... ttgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC
                                 aattttatgtcattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaggtccctttgttccatcagtcttatataagaaatgaataatgccgtgttgctcatctgttacatgtatcttttgaattttatgtcattgaatttagATTCAAGAGCTTGTAGAGGCAATTGTACTGCCCATGACACATAAAGACCGGTTCCAGAAGTTGGGTATTCGTCCTCCAAAAGGGGTTCTTTTGTACGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT