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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtccctcctaggttggtcaagtattttttagagtttttacttattcttcagtttatggtggttgtagctaatttgtttattcgctatttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT

Basic information

species Zea mays
transcript GRMZM2G104449_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 6
-----------aagtccctcctaggttggtcaagtattttttagagtttttactt--attcttcagtttatggtggttgtagctaatttgtttattcgctatttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT
           |     || ||     |  || |  |||| || |  ||||| ||  ||| |    || ||||  |||||  ||||  | |  || | ||||||||||||||||||||||||||||||||| ||||| |||||||| ||| |||| ||||| || ||| | || ||||||||||||||| | || ||||| || |||||||||
gttggctaaagataaatcttctttacagtccatgatttttctacaaattttagttggattttctctttgatggatgttgtgactaacatctgcatccactatttggaagaaagGGTGAAGGTTCCATGGCCAGTTTCGGAGAGAGAAGCTCTTCTTCACTACTTCGAATTAGAGTATCTTAAAGAAGATCTTGTCATTGTAATCATGAAAACT

upper sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G34940.1 (Glycine max), 3'ss of exon 6
aagtccctcctaggttggtcaagtattttttagagtttttacttattcttcagtttatggtggttgta-gctaatttgtttattcgctatttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT
  ||   |||    |    ||||||      | |      | ||| |   |  ||||      ||| | ||| |||| || | |   | |||||||||||||||||||||| |||||||  | ||   ||| || |||||  | ||||||| |    | || ||  || |||| ||  |  |  ||||  | |  ||  | 
--gtttgtccagcctgcaccaagtaaaaaaaaaaaac---atttaatgccc--tttaccacttttgaatgctgattt-ttcactgaat-tttggaagaaagGGTGAAGGTTTCATGGCCTCTGTCTCTGAGGGAAGCTATAGTGCACTATTATCTGTTTGAGTACTTTCAAGATGACTTAATTGTTGTTCTTACAAATTCG

upper sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G36220.1 (Glycine max), 3'ss of exon 5
--aagtccct-cctaggttggtcaagtattttttagagtttttacttattcttca-gtttatggtggttgtagctaatttgtt-tattcgctatt-tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT
    |||  | |||   |  || ||  |   ||||   |||    | | |   || | | |  |   ||     | | |  || ||||    ||| ||||||||||| ||||||||||||||||| |  |    || ||||||||  | || |||| |    | || ||   | |||| ||  | ||| || |  |  |||| || 
gtttgtctttacctgcatcagttaaaaaagatttactttttagtgtcactgaccatgctaaaagcctttacttttgaatacttatattgctcattgtggaagaaagGATGAAGGTTCCATGGCCGCTGGCTACAAGGGAGGCTATAGTGCATTATTATCTGTTTGAGTACTATCAAGATGACTTAGTAGTTATTCTTTTGAATACG

upper sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G10450.1 (Glycine max), 3'ss of exon 5
aagtccctcctaggttggtcaagtattttttagagtttttacttattcttcagtttat-ggtggttgtagct----aat-ttgtttattcgcta---tttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT
  ||   | ||   ||   ||| || |||||  |   |||   | | ||| |   |       ||| |  ||    |||  || || ||| ||    |||||||||||||||||||||| |||||||  | ||   ||| || |||||  | ||||||| |    | || ||  || |||| ||  | ||  ||||  | |  ||  | 
--gtttgttcttccttcaccaattaatttttttaacattttaatgtcctttaccatgccaaaagttttcacttttgaatgctgatttttcactgaattttggaagaaagGGTGAAGGTTTCATGGCCTCTGTCTCTGAGGGAAGCTATAGTGCACTATTATCTGTTTGAGTACTTTCAAGATGACTTAGTTGTTGTTCTTACAAATTCG

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|148983373|gb|EE029360.2|EE029360
EST:     TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG                         GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
genomic: TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAGgttggttgca ... tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
EST: gi|149078013|gb|EE166751.2|EE166751
EST:     TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG                         GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
genomic: TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAGgttggttgca ... tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
EST: gi|71429317|gb|DR810367.1|DR810367
EST:     TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG                         GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
genomic: TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAGgttggttgca ... tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
EST: gi|76014645|gb|DT941815.1|DT941815
EST:     TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG                         GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
genomic: TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAGgttggttgca ... tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
EST: gi|93284538|gb|EB676802.1|EB676802
EST:     TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG                         GGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT
genomic: TCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAGgttggttgca ... tggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcagtttatggtggttgtagctaatttgtttattcgctatttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT
                      agctaat  putative branch site (score: 3)
                         taatttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtccctcctaggttggtcaagtattttttagagtttttacttattcttcagtttatggtggttgtagctaatttgtttattcgctatttggaagaaagGGTGAAGGTTCCATGGCCGGTTTCAGAGAGAGAGGCTATTCTACACTATTTTGAACTGGAATATCTTAAAGAAGATGTCGTAATTGTGATAATGAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG