Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggctatacaattatcctaatattattatgaatacgaactccaaactcttgcacattactatgggtgaaagcggttagcatttccttgacttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG

Basic information

species Zea mays
transcript GRMZM2G017853_T01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017853_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g26920.2 (Oryza sativa), 3'ss of exon 5
--------------aggctatacaattatcctaatattattatgaatacgaactccaaactcttgcacattactatgggtgaaagcggt-tagcatttccttgacttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG
               | ||||    || | |||| | |   |  ||||  ||| | ||  ||||  |||||  ||||     ||  | |  | | |||||||||||||||||||||| ||||| |||||||| ||| |||| |||||||||||||||||||| |||||||||||||||||||| ||||| || ||||||||||||
atatcctcaattgatgactatttg-ttgttctaa-agtgcaagcaatattaacgc-aagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacAAAATAGATAGAGGTGCTCATTTTTTTTGGTTGAGGAAAGGAACTTTGGACACACGACCAGATCATATTATCAATCAAATTCATTATGAG
















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|74233405|gb|DT641319.1|DT641319
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|91871463|gb|EB401433.1|EB401433
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTATAT                         AAGATAGACAGAGGGGCACATGTTTTCTGGTTGAGGAAAGAAACTTTAAAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|211291636|gb|FL460652.1|FL460652
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|71437097|gb|DR818147.1|DR818147
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|18177348|gb|BM378558.1|BM378558
EST:     CAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: CAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|76927174|gb|DV171165.1|DV171165
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|71310881|gb|DR791743.1|DR791743
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|78089273|gb|DV517647.1|DV517647
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|78082079|gb|DV510491.1|DV510491
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGGACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|71310883|gb|DR791744.1|DR791744
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|74233404|gb|DT641318.1|DT641318
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|78085442|gb|DV513835.1|DV513835
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTC
EST: gi|211289510|gb|FL460651.1|FL460651
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|101382998|gb|EB813552.1|EB813552
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|78089274|gb|DV517648.1|DV517648
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|76927172|gb|DV171164.1|DV171164
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTTTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|71764490|gb|DR962427.1|DR962427
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC
EST: gi|78085441|gb|DV513834.1|DV513834
EST:     ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTAT                         AAGATAGACAGAGGTGCACATGTTTTTTGGTTGAGGAAAGGAACTTTAGAC
genomic: ATGTTGTTCTTGAGGCAGGAGGCTGTGTTCTCAGGCTGGCTGGACTTTATatatccccaa ... ttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgcacattactatgggtgaaagcggttagcatttccttgacttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG
                                    ttccttgac  putative branch site 
         attactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggctatacaattatcctaatattattatgaatacgaactccaaactcttgcacattactatgggtgaaagcggttagcatttccttgacttggacacacAAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA