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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt...

Basic information

species Zea mays
transcript GRMZM2G110983_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactt-tttaagattccaaagca-tgtt-----
          ||||||| |||||||| || ||||||| |||||| ||||| ||||| ||||| || ||||||||||||||| ||||||| |||||||||||||||   | ||||     | |||| |   |||| |  |  ||     | ||   |||  |    | | | | ||| || | |   ||| |  | || |  |     
----------GTACGTTCAAGCTGACACTTCAGTTTACTGAAGATTATCCTAACAAGCCACCTACAGTGCGATTTGTTTCTCGGATGTTTCATCCTAACAgtaagcc-tctctccctgctgttta-atacttgcctgtggcatg----gttcctgtttcttacaagttataa-gtatttatgtggcatttcggaacaatagtctaac

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G16160.1 (Glycine max), 5'ss of exon 5
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagt-tgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt---
          ||||||||||| |||| || |||||||  || || ||||| || |||||||| |||||||| ||||||||| | ||||| |||||||||||| |||      ||   |   | || ||   | |  | ||||  |   | |  |||  ||   || | |   ||  |    | | | ||        | ||   
----------GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaaaactaccctgcaattccactttggagttagaatgacaatcacgtgaaatt---tttg-tacaatcaatacctgagggttatccttacttttaaa

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          | ||||||||| ||| ||| || |||| ||| || ||||||||||| ||||||||||| |||||||| ||| | ||||| || || ||||||||||| |   |     | ||| |      ||   |  |||| |  |     | |  |     |  | |  | |||| |   |                
----------GCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACAgtaagttttaggtggaaaagattaatcttcatgtccat-aaattacctatgtagctactaatgccatttt--tctactctgggaag--------------

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G34170.2 (Glycine max), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattc-caaagcatgtt
          | ||||| ||| ||||||||||||||| ||| || |||||||| ||||||||||||||||||||||| ||| | ||||| ||||| || |||||||  |   |     || |||||    ||| |  |  ||||| || | |||         | ||| | ||  | ||||| |  |||    ||      
----------GCACGTTCAAGTTGACTCTCCAGTTTACTGAGGATTATCCAAATAAACCACCAACTGTGCGATTTGTGTCTCGCATGTTTCATCCAAATAgtaagtattaggtggaaaatctttacg---ttggagtatcaataaatttagctg-------tgtagctctaattcattttttcaacttcgtgtag------

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G40860.1 (Glycine max), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgca-taagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          ||||||||||| |||| || |||||||  || || ||||| || |||||||| |||||||| ||||||||| | ||||| |||||||||||| |||        | ||   | | | |  ||| |   |  ||| |  |||  |  || |    ||  | |  | |      | |    |  | |  | | 
----------GTACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGCTTTGTTTCTCGAATGTTTCATCCTAACAgtgagtacaaaactaccctgctattccactttggagctaacaatcatgtgaaatatttgtacaatcattttttt-tgtacaatcaatacctgagggttatc

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G01270.1 (Glycine max), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          | ||||||||| |||||||||| |||| ||| || ||||||||||| ||||||||||| |||||||| ||| | ||||| ||||| ||||||||||| |   |     | ||| |      |       |||| |  |     | |  |    ||  | |  | |||| ||  |                
----------GCACGTTTAAGTTGACTCTCCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagttttaggtggaaaagattaatcttcctatccgt-aaattacctatgtagctactaatgtcatttt--tctactcttggaag--------------

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G16160.3 (Glycine max), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagt-tgtttctcatccatatttacaagattgcataagaaataagttgatctga---ttttgtct--tcgctgtgatgtactttttaagattccaaagcatgtt
           |||||||||| |||| || |||||||  || || ||||| || |||||||| |||||||| ||||||||| | ||||| |||||||||||| |||      ||   |   | || ||   | |  | ||||  |   | |  |||   ||||||    ||  |         || |    | |   || |     
-----------TACGTTTAAGTTGACACTTCAGTTTACAGAGGATTATCCTAATAAACCACCTACTGTGCGTTTTGTTTCTCGAATGTTTCATCCTAACAGtgagtacaaaactaccctgcaattccactttggagttagaatgacaatcacgtgaaatttttgtacaatcaatacctgagggttatccttacttttaaac-----

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagt-tgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          |||| || ||  || | || ||||||   ||||| |||||||| ||||||||||| ||||| ||||||||  ||||||||||||| ||||||||||||    | ||| | ||  | |   |   |     | ||  | |||||       |    | || || |  |  || |                  
----------GTACTTTCAAATTGTCACTGCAGTTTTCGGAAGATTATCCAAATAAACCACCAACAGTGCGGTTTGTTTCACGGATGTTCCATCCAAACAgtaagttggagattatc-acatc-atagtttcttactctgagtacatgtgatcaacgaaagctcacact-tggtcaatgttgtgcag--------------

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatct---gattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          |||| || || ||  | || |||||   |||||| ||||| || ||||||||||| || || ||||| ||  ||||||| |||||||| |||||||| |       | | |||     ||||   ||   |    |||||| |   | ||||| || |  | | | || ||| |      | |   |  |   
----------GTACTTTCAAACTCTCACTGCAGTTCTCTGAAGATTATCCCAATAAACCACCAACAGTTCGGTTTGTGTCACGGATGTTTCATCCTAATAgtaagttatagagatacaacatt----ggattttctatccacctggttgatgttcagcttttgcctccaat-taacgttcttctgctctattcgttgtgtag-

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt----
          |||||||||||||||| || ||||| |  || || |||||||| || || ||||||||  ||||||||||| | ||||||||||| || |||||||||      |  || ||||    ||  ||  |    ||      || | ||  | | ||   |   |  |  ||| |||   |    | ||| |     
----------GTACGTTTAAGCTGACACTTCAGTTCACAGAGGAGTATCCAAATAAGCCCCCAACTGTTAGATTTGTTTCTCGAATGTTCCATCCAAATAgtaagttgagagaaaggcaaatttttgtgaaagctaatttgattgac--atttcatgatatgtttatta--actttatttataaccatgtgtatcatataccac

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 4
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatattta-caagattgcataagaaataagttgatctgattttgtcttc--gctgtgatgtactttttaagattccaaagcatgtt
          ||||||||||  |||| || ||||||   || || |||||||||||||||||||| ||||||||||||||  | ||||||||||| || |||||||||   ||       | |||  |  | | |||   |||||  ||  | |   |  |  |||   ||   |  |  | |||   |||    ||      
----------GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATAgtaagttggaactatgttgcaattagtatcacttcatgttaaata--tttctttagctgcggtttcttacttctaccttttattttgaattggccag------

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 5'ss of exon 5
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttc-gctgtgatgtactt--tttaagattccaaagcatgtt-
          ||||||||||  |||| || |||||||  || || ||||| || || ||||||||||| || ||||||||||| ||||||||||| || |||||||||        | | |  ||     || |  ||     |  || |  |      ||  || ||    || | | |  | |   | |    | | ||   
----------GTACGTTTAAATTGACGCTTCAGTTTACAGAGGATTATCCGAATAAGCCACCAACTGTACGCTTTGTTTCTAGAATGTTCCATCCAAATAgtaagttggacg----caagaactatgcttttacccaattctcactttcaattatgagagttctcagccaacatatgcctaatgtgcaaatatgtaacgtgcca

upper sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ21576 (Selaginella moellendorffii), 5'ss of exon 3
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt
          ||||||| ||||| ||  | ||||| |  || || ||||| |||||||| |||| ||| || ||||| || | |||||||||||| |||||||||||  ||   || | || |  | |  || | || |   |                                                         
----------GTACGTTCAAGCTTACGTTACAGTTCACGGAGGACTATCCCAACAAACCGCCAAATGTCCGGTTTGTGTCGAAGATGTTCCATCCCAACAgtaagttcgttt--attcgtagtgtctatcttccttacgcgctctcgcag--------------------------------------------------

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|31998321|gb|CD662030.1|CD662030
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|37400480|gb|CF637593.1|CF637593
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|50323647|gb|CO518773.1|CO518773
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|37376281|gb|CF624651.1|CF624651
EST:     AAACAAACCACCAACTGTGCGA-TTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|37384502|gb|CF629329.1|CF629329
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|37390719|gb|CF632593.1|CF632593
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|33104117|gb|CF064077.1|CF064077
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAATA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|148995969|gb|EE035217.2|EE035217
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
EST: gi|32846308|gb|CD985989.1|CD985989
EST:     AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA                         TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC
genomic: AAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtt ... tcatatgcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTCTCAGGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACAgtaagttgtttctcatccatatttacaagattgcataagaaataagttgatctgattttgtcttcgctgtgatgtactttttaagattccaaagcatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG