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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccattcttttatcttgcccttgtttttcaacctagcacatgtcaagatattgattggcttccatactttgaggttttagtgacaaacttaggcgtctgacttataattcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGTTGGGTGAACTCTACAACCACAGTAGAGGTTATCTTGTAAA

Basic information

species Zea mays
transcript GRMZM2G018508_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 6
gtccattcttttatcttgcccttgtttttcaacctagcacatgtcaagatattgattggcttccatactttgaggttttagtgacaaacttaggcgtctgacttataattcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGTTGGGTGAACTCTACAACCACAGTAGAGGTTATCTTGTAAA
                                    |  ||| |||  || |        |||  || || |    ||  ||  | ||   ||   | | |  |  ||||||| |||||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| |||||||| |||||||||| ||||||||| |||||||||||
------------------------------------gtgcat-tcatcatctatgcctttttctttatttagtcaattgggttgcgaaa--agtattttaatctgaaattctttcagAAACACAACATCAATTCTCTGCTCGAGAAAGTGATTGGGGTTTTACTTCCTTTATGCCTTTGGGTGATCTCTACAACCCCAGTAGAGGCTATCTTGTAAA

upper sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtccattctt--ttatcttgcccttgtttttcaacctagcacatgtcaagatattgattggcttccatactttgaggttttagtgacaaacttaggcgtctgacttataattcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGTTGGGTGAACTCTACAACCACAGTAGAGGTTATCTTGTAAA
  |   ||||||  || | ||     ||     | |  | |    ||   || |   |   || |||||   | | |  |||          |   ||||    || |||     ||||||| || ||||||||||||  ||||||||||||||||||||||||||| ||||| |||||  |   |||  | ||  | |     | ||||| ||| || ||
gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttggg---ggattccacggtcttatatttc---------ccatggcg----acctat-----ttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
















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|50332270|gb|CO527396.1|CO527396
EST:     CAGCCTCTCTGTGGTTAATCAAATTCACAACAAATTCACAATAAGAAAAG                         AAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCAT
genomic: CAGCCTCTCTGTGGTTAATCAAATTCACAACAAATTCACAATAAGAAAAGgtccattctt ... attcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatactttgaggttttagtgacaaacttaggcgtctgacttataattcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGTTGGGTGAACTCTACAACCACAGTAGAGGTTATCTTGTAAA
                                 gtctgac  putative branch site (score: 3)
                                              ttcttgc  putative PPT
                                        ttataattctt  TA-rich tract