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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
----tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatca-gtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
       |  ||  ||| ||  | ||||||   ||| | | |   |  | |   || |  | |   ||     || ||||| || |  | || | | ||||||||| ||||| || ||||||||||||||||||||||| ||  | |||||||| ||||||||||||||||| ||||| ||||| || ||||| || |||     
ttgcccgaaagttgtgt-caaatgacttgagcattgcttttttcacaaggtggttttgatatcatgata----tgcatcttaattacatgtgtttcttgtttcagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 1
tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgttt-----cagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
    | |        ||||   | |   |||  | | |    | ||||| |    |||   |||  |   || || |||| | |   ||   ||| |     ||||||||||||| || || ||||| |||||||| || ||  |||||||||||||||| ||| | ||||| || |||||| | || || |||||||| |    
----gcgaaagagggatttggttggtgcttttatatctgaattagattt-tggttcaggataatgtgaaagtttcctgattattgaccttattgtctttctacagTGGACATAATTTCAGCTATTGAATTTGACAAGTCCGGTGATCATCTTGCTACTGGTGATCGGGGTGGTCGAGTGGTTCTCTTTGAGAGAACAGATACAAA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 1
tttagtgtcttgttcatttcacttgatatttgttgtgtc-ggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgttt-----cagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
    |          |||||  | | |  || |||| || |  ||  |||||    ||    |||  |   || || | || | |   ||   ||| |     ||||||||||||| ||||| ||||| |||||||| |||||  |||||||||||||||| ||| ||||||| || |||||| | || || |||||||| |    
----gcaaaagaggaatttcg-tcggtgctt-ttgtatctgaattagtttgtggttcaagataatgtgaaagtttccttattattggccttattgtcttcctacagTGGACATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGAGGTGGTCGAGTGGTTCTCTTTGAGAGAACAGATACAAA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 1
--tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgt-ttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
  |  ||  |     |        |||| ||   |||  |  |||    ||| | |  |  |   | |||||     ||  | |      |  || | ||||||||| ||||| ||||| ||||| |||||||| |||||  |||||||||||||||| ||| | ||||| || || ||| | || ||  | ||||| |    
tgtgaagcctgccagtatgagtgattgacata-attggattagctattgttgct-gttaa-tgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 1
--tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgt-ttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
  |  ||| |     |  |     |||| ||   || | |  |||  |||  | |      |   | |||||     ||  | |      |  || | ||||||||| ||||| ||||| ||||| |||||||| |||||  |||||||||||||||| ||| | ||||| || || ||| | || ||| | ||||| |    
tgtggagtcttccagtattagtgattgacata-attatattagct--attgttgcagttaatgtgtaagtttcctaattatttacccaattttatttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAACGGACAGATACAAA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
tttagtgtcttgttcatttcacttgatatt-tgttgtgtcggcttg-atttgttcgccagctaaatcagtttgtatcttg-atcagtatgctacatgttt--cagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
      ||   | | | ||    ||  ||| ||  |||| |  | | |  |||        |    || | ||| | | | | |  ||  |  |||||||  |||| ||||| || ||||| ||||||||||||||| ||||  | |||||||| ||||| ||| | || ||||| |||||||| || ||||| |||||||    
-----cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 1
-tttagtgtctt-gttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
  | | | | || | ||||     ||   |||| |      || |  | |||           ||  ||||||| | ||   ||   ||    ||  | |||| || || ||||| || ||||||||||| ||| ||||| | |||||||||||||||||| | || || || |||||||| ||  | ||||| || |    
gctgactttgttaggtcataattgttcgcatttttctcacaggttaaaattgagttattttctaactagtttgtctattttccaac-tgtcctat-ctacagTTGATATCATATCAGCTATTGAGTTTGATAAAACTGGGGACCATCTTGCTACTGGAGATCGTGGGGGTCGGGTGGTTTTATTTAACAGAACTGATACGAG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S138_11V6.1 (Physcomitrella patens), 3'ss of exon 1
-tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccag--ctaaatcagtttgtatcttgatcagtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
  |||    |        | || |   | |   |   || || |  ||  ||  | | |   ||||||   ||||| |||  ||     | ||  | |  |||| || || || || |||||||||||||| ||||||||| | ||| | || ||||| ||| |||| |||||||| || ||||| || ||||| ||    | 
gcttaagaacgctaaagctgcaatgagtttgcttccagtaggttccatacgtatgtctgacttaaatctagttgtaactt--tctactcgttat-tatggcagTCGATATCATCTCGGCAATTGAGTTTGATAAATCTGGGGAACATTTAGCAACTGGGGATCGAGGAGGACGTGTTGTGTTGTTTGACAGAACGGATGGCGT

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|37419039|gb|CF647193.1|CF647193
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGC
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGC
EST: gi|89250814|gb|DY622600.1|DY622600
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
EST: gi|91873992|gb|EB403949.1|EB403949
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
EST: gi|60340196|gb|DN207169.1|DN207169
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATCTCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
EST: gi|148939774|gb|EC884472.2|EC884472
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
EST: gi|148991720|gb|EE033282.2|EE033282
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
EST: gi|94472892|gb|EB701850.1|EB701850
EST:     GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATG                         TGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA
genomic: GTTTGCGCAGGTCTTCGGCGAGCGCGCCGCGGGAGAAGATGTGCAAGATGgtaataaatt ... catgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
              taaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtgtcttgttcatttcacttgatatttgttgtgtcggcttgatttgttcgccagctaaatcagtttgtatcttgatcagtatgctacatgtttcagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - ttcattt
- - - - - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - - - cggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct