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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcatacccttattttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG

Basic information

species Zea mays
transcript GRMZM2G174644_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 5
gttggtgatatgaatgtcattgcagatatcttgaatggagacagctt-tgtcaacaaattttgctaatta-------------tgcatacc----------------cttattttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
||| ||||||| |    ||||||||| | |||   || | ||| ||| || || | |||  ||||  ||              ||||| ||                 ||||||| |||||||||||||||||| || |||||||  |||||||| || |||| ||||||||| || || ||||| || |||||||||||||| || ||||| || ||  
gttagtgatatca---ccattgcagaaaccttc--tgcaaacatcttctgccagccaatgatgctggttccacagttctttactgcatgccatcgataatttttcattttattttctcagGTAAGCCATCATCCTCCGATGGGTGCCGCTCACTGTGAAAATGCACATTTTACATATGACATCACCTCCAAGTTGAAGACCAAATTCTTGGGGAACTCTC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
---gttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcataccct---tattttg----tcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
    || || |  ||| |        || |  |   || | | |  | |||    ||   | |  ||   |||  |||       ||||||     |||||| || ||||||||||||||| ||| ||| ||   ||||||||| |||||||| || ||| | || || |||||||| || |||||||||||||| || |
ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 5
---gttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcataccct---tattttg----tcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
    || || |  ||| |        || |  |   || | | |  | |||    ||   | |  ||   | |  |||       ||||||     |||||| || ||||||||||||||| ||| ||| ||   ||||||||| |||||||| || ||| | || || |||||||| || ||||||||||||||||| |
ttattttgtaaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctctgtgtatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAATTCTG

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 5
---gttggtgatatgaatgtcattgcagatatcttgaatgga-------gacagctttgtcaacaaattttgctaattatgcatacccttattttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
     | || |  ||||     ||   || || |  | |          |  | |||   |   | |||       ||||  |||   || |  |||||||| || || |||||||||||| ||| ||  ||    |||||||| |||||||| || ||| | || || ||||| ||||| ||||||||||||||||| |
ttgcattgttaggtgaacacttttaaggaaatttcaatttctcttctctgttatcttctcccttatattggatatcttatagatatatttttaatgtcagGTGAGTCACCATCCCCCAATGAGTGCTGGGCATGCTGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTAAAGACTAAGTTTTTGGGAAATTCTG

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|22491096|gb|BU051019.1|BU051019
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGGGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|19351392|gb|BM895924.1|BM895924
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|74244334|gb|DT652248.1|DT652248
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|78025234|gb|DV493621.1|DV493621
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|50328677|gb|CO523803.1|CO523803
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|149078287|gb|EE167049.2|EE167049
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|211454955|gb|FL196639.1|FL196639
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|71326510|gb|DR799932.1|DR799932
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|94475418|gb|EB704376.1|EB704376
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|148995971|gb|EE035219.2|EE035219
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|20507134|gb|BQ279500.1|BQ279500
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|28909493|gb|CB331845.1|CB331845
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|76011657|gb|DT938827.1|DT938827
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|78116426|gb|DV534813.1|DV534813
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCCCTGCGAGAATGAACATTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTT
EST: gi|71326507|gb|DR799931.1|DR799931
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|149084040|gb|EE173435.2|EE173435
EST:     AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCCATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: AGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
EST: gi|5499280|gb|AI855147.1|AI855147
EST:     CAGGGCATTACATTTCTTGCTGAGCAG                         GTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT
genomic: CAGGGCATTACATTTCTTGCTGAGCAGgttggtgata ... attttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagacagctttgtcaacaaattttgctaattatgcatacccttattttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
                         tgctaat  putative branch site (score: 2)
                                        cccttatttt  putative PPT
                   aaattttgctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcatacccttattttgtcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA