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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgttattattggcgagtttctgcagaagcggggaacaacatcgtgcttccacatgtacagtttactcaagatacaataatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG

Basic information

species Zea mays
transcript GRMZM2G107629_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
gattgttattattggcgagtttctgcagaagcggggaacaac--atcgtgcttccac-atgtaca-gtttactcaagatacaat--aatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG
     ||| || ||    |||| ||        |  | ||||   || || ||  || | | | | ||   ||  |  |  | |  ||| |  ||    | |||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||| |||||||||| ||||| || || ||||| ||||| || ||||| || 
-----ttactactgatt-gtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC

upper sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 6
gattgttattattggcgagtttctgcagaagcgggga--acaacatcgtgcttccacatgtacagtttactcaagatacaataatgtgtttgcact----ttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG
       |  ||   ||| |    |    | | |  |  |  | | |  |  |       | |||| |   |  | |   ||  ||| || |||      |  |||||||||||| || |||||||| ||||| || |||||||| ||||| |||||| |  | || || ||  |   | | |  |  |||||| | || ||  | 
------caagatacccgaatgaaagtgctacctgatataattaaaccacgtctttgttgttgcagtatgaccttgttgtgatcttgttttggcatcaatgtaacagGTGTGAAGCATTTTCGACCTACCCTCGTACTTATGATCTGCTCCATGCATGGACTATATTTTCTGATATTATTGAGAAGGAGTGCAGTCCAGAGGATTTA

upper sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 7
gattgttattattggcgagtttctgcagaagcggggaa----caacatcgtgcttccacatgtacagtttactcaagatacaataatgtgtttgcactttg-cagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG
  || || | ||    ||   |  | | |  || | ||    |||| | |   | ||   | ||     |  |    ||    | |||  | |  |   || |||||||||||| || || ||||| |||||||| |||||||| ||||| |||||| | || || || ||  |   ||| | ||  |||||| | || ||  | 
-gtttttttaatgaatga---ttagtaaacacgtgaaatcttcaacgttgaattacc-tttttatgaccttatatcaatgatgttatgcatataaatgctgacagGTGTGAAGCTTTTTCAACCTACCCTCGAACGTATGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA

upper sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
-gattgttattattggcgagtttctgcagaagcggggaacaacatcgtgcttccacatg-tacagtttactcaagatacaataatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG
 |||| | |    ||  ||  |  ||   ||  |   |   | |  |   ||  |  || || |  ||       |    |     || || |  || ||||||||||||| |||||||| |||||||| || |||||| | |||||||| ||| | || ||||| ||| | || || | |||||| |||||||| || |||
tgattataaaccatgagga--tggtgtgaaaaagaaaattgaaactgaagtttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG

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|87157567|gb|DY402356.1|DY402356
EST:     ACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCATGACTG                         GTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATG
genomic: ACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCATGACTGgtatgtgtta ... cactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATG
EST: gi|22935914|gb|BU572189.1|BU572189
EST:     ACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCATGACTG                         GTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATG
genomic: ACCCTCAAGATAATCTATGATAGAGGGCTGATAGGCAGCAATCATGACTGgtatgtgtta ... cactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttccacatgtacagtttactcaagatacaataatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG
                            atacaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgttattattggcgagtttctgcagaagcggggaacaacatcgtgcttccacatgtacagtttactcaagatacaataatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA