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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcag

Basic information

species Zea mays
transcript GRMZM2G174644_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 8
AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactg-gtcatacttgattgactgcag
|||||||||||| ||||| || || ||||||||| ||||| ||||||| || ||||| || ||||||||||||||||||||||| || ||||| |||||||||  | ||||||    | ||   || ||   | ||| | ||||||||| |  |  |    ||  |||  |  |   |||  || ||||  ||  |  |||   |    | ||||||  |   | |   
AGAACCCAAAATAATGATAACTGGAAAGTGGAACCAGTCCATGAGTTGTCAGCCATGCGATCAAGAAGGCGATCCTCTTCCAGGAACTGAGCTAAAGGAGgtcagaatttcttcggatgtccattattacacagaacatttgttatataaaggcaaagctaat-taatacttctataataactgtggatatcttctcaactcttcaacattatactttgtcc-cag---

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 5'ss of exon 8
AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcag
||| ||||| ||  | || || || || |||||| ||||| ||||||  || ||||||||    |||||||| |||||||||||||| || |||||||||||  ||     ||      |||   |  |        |  |  ||||| ||  | | |        ||| |  |  || |                                                
AGAGCCCAAGATGCTAATGACCGGAAAATGGAACGAGTCCTTGAGTTATCAGCCATGTGATGCGGAAGGCGAACCTCTTCCAGGCACCGAACTGAAGGAGgttttatcaatttctctcctcta--agcaaaccctctgcatactatatctagtcacctttctaattatgttacttccacag-----------------------------------------------

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 8
AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcag
 |||||||||||  |||| |||||||| |||||  ||||  |||||| |||||||||||||   ||||| || |||||| ||||||| || |||||||||||  || | || || | |||  | |   ||        | |||| |   | | |   | | ||    || || | | || || ||    || || |||  || |||| |   |               
GGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgt--taatctcattgaattta-gttttcat------tatttgttgt---tgtgcaagtcaaatat--tgttgcttatattttagcta--gaatgctgccatgcactgatttgaacc------------

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|213172926|gb|FM184971.1|FM184971
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTACCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|31349767|gb|CD434124.1|CD434124
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|211409590|gb|FL109891.1|FL109891
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|78025234|gb|DV493621.1|DV493621
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACA
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACA
EST: gi|211409591|gb|FL109892.1|FL109892
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|213167873|gb|FM190575.1|FM190575
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|78116425|gb|DV534812.1|DV534812
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|83278633|gb|DV942641.1|DV942641
EST:     TGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: TGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|60343663|gb|DN210636.1|DN210636
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|76011658|gb|DT938828.1|DT938828
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|211409595|gb|FL109896.1|FL109896
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
EST: gi|5499280|gb|AI855147.1|AI855147
EST:     AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACAC

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: 198

AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 364

AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 456

AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 217

AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtacttt ... ttgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCATGTGACCAAGAAGGCGATCCTCTTCCAGGCACGGAGCTGAAGGAGgtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG