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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG

Basic information

species Zea mays
transcript GRMZM2G109725_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g01660.1 (Oryza sativa), 3'ss of exon 2
-----------gtacaatccc---ctgcagcccccctctccggtaattagaggg-aagcaattacttttccaatcttat--gcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
            | || | |        | |     | || | | ||| ||||| || |||||  || ||||  |||||  ||  |||| ||    |    || |  | ||||    ||||||   ||||||||| |||| |||||| |||||||||||||||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||||||||| || || |
gtatgacccctatgcatttctagatcataactattttttctgtttattggaggggaaacaattg-ttctccagccttatcagctattcatttggttccaatttaatttcattg----tgaactc--acagGCGTTGAAGAGTTATATTTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCCATGTTTTGCCCTATGATATGTCGAGAGATAG

upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
      |  | ||  |  |     |     ||   |    |  ||| |   ||     ||    |      | ||     ||  || |   ||    |||    ||   |       | ||  | || |||||||||||     | |||||||| ||||||||||| ||||| ||||| || ||||| |||||||||||||| |  ||| |     
------tatcgtgttgttctgaaattta-caacatggtaaagtcaagtttattgttgttccctgggtagctagtttg--ttgatttcactctacctttggcatgcttagA-------TGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC

upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
              |   |     |    | ||||||     |  |   |   |  | | || |  |  |   |      | | ||||  | | |     |   | ||     |   | ||  | || |||||||||||     | |||||||| ||||||||||| ||||| ||||| || ||||| ||||||||||| || |  ||| |     
-------------tacttctagattataatgattagaacatggtgaagtcaagtttattgttgt-tgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagA--TGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC

upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactata-acagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
                 |  | || |   | |   |||  |   | | | ||||| | |  | |  | ||  ||       | ||  |  |   | | ||||   |  | | || |  | ||| | || |||||||||||      ||||||||| || |||||||||||  | ||||||||||||||||| |||||||| ||||  ||  |  
-------------ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaa-gactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA

upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G61415.2 (Arabidopsis thaliana), 3'ss of exon 2
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
     ||     |      |    |   |||  | |||      ||| | |  |  |   ||   |  ||  |   || ||   |  |  || || |||||  |  |  | ||  | | ||  | ||||| |||||| |      |||||| || || || ||||||||  | ||||||||||||||||| |||||||||||||  ||| |  
-----attttaagtgttatcttctttatgta--tggagtttttgaatgattagttgagcttttacc--ttgcaccaagactaatt--actttttttgtggt--atcaacatagATGATGAAATCCTATATATGGCTTGAAACTGCTGATGGCTCAATCCAACAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATATGTCAAGAAGTAA

upper sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
               |     || |  |||  ||               ||| | || ||||   |  ||   |   |||| | || |  || ||     |    | || || |   | ||| ||||||||||||| ||      ||||||||| ||||| ||||| || || |||||||| ||||| |||||||||||||| || |||||     
------------tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaattg--tgtatcaagA--TGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC

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|211041297|gb|FL239839.1|FL239839
EST:     GGTGTTCGGCAATAATGTCGGAGAGCGAGTTAGCAGTAATAAAACCAGAG                         GCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAA
genomic: GGTGTTCGGCAATAATGTCGGAGAGCGAGTTAGCAGTAATAAAACCAGAGgtacaatccc ... actataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
                                            aactataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG