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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcaaactctcaaataattaatcaaacaacaacagagacagacagacaaattgatgaaatgaactaattaattaatgaactgaatctatatccaacatgatatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT

Basic information

species Zea mays
transcript GRMZM2G059083_T01
intron # 5
splice site 3'
intron type U2

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|78085944|gb|DV514337.1|DV514337
EST:     TCCGCTCCTTCTTGTGGAAGATGTTTTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|76935133|gb|DV174192.1|DV174192
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|5791146|gb|AI977938.1|AI977938
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|13150081|gb|BG320403.1|BG320403
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTCGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|74238896|gb|DT646810.1|DT646810
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGCCCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|148968309|gb|EE019500.2|EE019500
EST:     TCCGCTCCTTCTTGTGGAAGATGTTTTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTTCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|78021596|gb|DV489983.1|DV489983
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|78085945|gb|DV514338.1|DV514338
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACTAT-GGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCT
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTAC-ACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCT
EST: gi|13315987|gb|BG410434.1|BG410434
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|5791046|gb|AI977838.1|AI977838
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|13315986|gb|BG410433.1|BG410433
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|13515779|gb|BG518055.1|BG518055
EST:     AGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: AGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|13249967|gb|BG360872.1|BG360872
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|14208424|gb|BG842102.1|BG842102
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|71420120|gb|DR805018.1|DR805018
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|31405961|gb|CD484693.1|CD484693
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|6918750|gb|AW400280.1|AW400280
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|8665396|gb|BE186212.1|BE186212
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|94474502|gb|EB703460.1|EB703460
EST:     CCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGGA-CACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: CCGCTCCTTCTTGTGGAAGATGTTCTTCGA-GGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|89249821|gb|DY621607.1|DY621607
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTGGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCTTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|76015964|gb|DT943134.1|DT943134
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
EST: gi|14569158|gb|BI097481.1|BI097481
EST:     AGATGTTCTTCGAGGAGCACGAGGACTACAAG                         TACACCGGGCTCGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG
genomic: AGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTG

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: 42 (upstream exon), 49 (downstream exon)
Score: 36

CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 25 (upstream exon), 26 (downstream exon)
Score: 2

CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAGgtctcaaact ... atatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatgaactaattaattaatgaactgaatctatatccaacatgatatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT
          taattaattaatgaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcaaactctcaaataattaatcaaacaacaacagagacagacagacaaattgatgaaatgaactaattaattaatgaactgaatctatatccaacatgatatacatagTACACCGGGCTGGCGTGGCTGTTCCTGGGCGTCCCGACCAGCGACACCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG