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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggacaatgttaaattaattgtggctcagtactatcttcttctgcataaagattatgcatgtatgcacttctgttgatttgttctcacttttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT

Basic information

species Zea mays
transcript GRMZM2G156800_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156800_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 3'ss of exon 3
ttggacaatgttaaattaattgtggctcagtactatcttcttctgca--------taaagattatgca-----tgtatgcacttctgttgatttgttctcacttttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT
            |   ||| | ||  | |||||| || ||||||  |        ||||||||||| |     ||      ||  | |||| | | |||||||||  ||||||||||| || |||||||||||||| ||||||||||| || ||||||||||| |||||||||  |
------------attgtaactctgcttgagtactctcctcttctataattatatctaaagattatgtaagttctgcccttgctctttttgactggatctcactttg-tttcagGAAATAAAATTTCTTAGTCAATTCAAGCATGAAAACATAGTGCAGTACTACGGCAGTGAATAT

upper sequence: GRMZM2G156800_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g11240.t01 (Vitis vinifera), 3'ss of exon 2
------ttggacaatgttaaat-taattgtggctcagtactatcttcttctgcataaagattatgcatgtatgcacttctgttgatttgttctcacttttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT
      | |||  |       | | ||  |||||   ||     | | | ||  |   ||  |||  | | |     |   |  ||||  |||| ||       |||||||||||  ||||   ||| || ||||||  ||||||||||||||||||||||||||||| |
tccaaataggattactaggcttctgatcatggcttcataaacattccctttgttttttgaaaatgt-tttgtatttcttactcaattttctctcgctg------cagGAAATTAAAGTTCTCCATCATTTAAAGCATCCAAATATTGTGCAGTACTATGGCAGTGAAATT
















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|87156020|gb|DY400809.1|DY400809
EST:     TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
EST: gi|22542085|gb|BU092523.1|BU092523
EST:     TGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: TGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
EST: gi|22473422|gb|BU037902.1|BU037902
EST:     AATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: AATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
EST: gi|50338068|gb|CO533194.1|CO533194
EST:     TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
EST: gi|87157200|gb|DY401989.1|DY401989
EST:     TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
EST: gi|26558715|gb|CA830950.1|CA830950
EST:     TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAG                         GAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT
genomic: TAATTCCAGATGATGCTAAATCAGTCGAGTCTCTGAAGCAATTGGAACAGgtatggtttt ... tttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaagattatgcatgtatgcacttctgttgatttgttctcacttttctttcagGAAATTAAGTTTCTTAGTCAATTTAAGCATGAAAATATTGTGCAGTACTATGGCAGTGAAACT
                                     ttctcac  putative branch site (score: 2)
                                 tttgttctcacttttc  CT-rich tract
                                            ttttcttt  TA-rich tract