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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaagaaagtagtcaatagtcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG

Basic information

species Zea mays
transcript GRMZM2G095887_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095887_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 3'ss of exon 21
gtaaaaagaaagtagtcaatagtcatatcattggatgcattaggaggctttgctaaatgtttt--cctggtttctatca--atagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
        ||   | |  || |||||    |||  ||  ||   |  | ||| || ||  |||  | | |||| | | |  | ||||||| || ||||| ||||| || |||||||| |||||||| || ||||| || || |||||| | |||||||||||||||||| | |||
------gtaatacaatgcattgtcat----ttgcttgtcttgaaatacgttgatacataatttgccattgttttttttatcacagATCCGCGCCCAAAGCACACATTTTTTGAGAGGCTTTCAACAACTAATACCGAATGAATGGATTAACATGTTCAATGAACATGAATTCCAG

upper sequence: GRMZM2G095887_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 20
------------------gtaaaaagaaagt--agtcaatagtcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                   | |   || | |   ||   |    ||   | |  |  |||        |    |||   |  |  |  ||  | |    |||| ||   ||||||| |||| |||||||| || ||||| || ||||| |  || ||||||||||| ||||| |||||||||||| |||||
tatatactctatctctatctgatgtgacacttgggtttttccaaatgcaaatcaactcatgtttcaattacaataataataataataatta-tgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATTCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

upper sequence: GRMZM2G095887_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
-----------------gtaaaaagaaagtagtcaatagtcatatcattggatgcattagg--aggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                  |  |   |||||      | |   | |          || |    | | ||   | |  |  |       || | |    |||| ||   ||||||| |||| |||||||| || ||||| || ||||| |  || ||||||||||| ||||| |||||||||||| |||||
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

upper sequence: GRMZM2G095887_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 21
gtaaaaagaaagtagtcaatagtcatatcattggatgcattaggaggct-ttgctaaatgttt-tcctggtttctatcaat---agATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
|| | |      |  |||    | ||  | |   |  | |       || |||||  | | |  |      |   |||| |   |||| |||   |||||||| || |||||||| |||||||| || ||||||| || |||||||||||| |||||  |||| |||||| |||||
gtgagatcgcctttttcatagttaattccttcaaactcttccttgaactgttgcttgacgctaatatcaaataacatcactttcagATACGTCAGCAAAGTACTCATTTCTTGAGGGGTTTTCAGCAACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAG

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|18384464|gb|BM417663.1|BM417663
EST:     TGTGTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCA
genomic: TGT-TATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTATCAGgtaaaaagaa ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                        tgctaaa  putative branch site (score: 2)
                                 ttttcctggtttct  putative PPT
                           taaatgtttt  TA-rich tract