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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacgcctgcgcgacacacacacatagccatcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC

Basic information

species Zea mays
transcript GRMZM2G065696_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065696_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 4
-----------------gtgac-gcctgcgc-gacacacacacatagcc---atcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC
                 ||  |  || | || ||  ||     ||   |   || | |||    ||| |       || | | |        |||||  |  ||   || | | |||||||||||||||||| || |||||||| ||||||||| ||||||||||||| || ||||||||||| |||||||| ||||||||||||||||||||     
gtagccatctgcgtactgtagccacccgagctgaatcagttcgatgatctacatgatcttgacatgtaatgtattcaagctgaaccgattcagctgatgaaactgtatt-tgtttcagGTGTTCTGCTGCTTTGGTAACTCGGTGGCTTCAACCAGGTTCCTGCTGCAAGATGAGTTCAACATTCAGACAACCCAGTGCGACAACTGCATCATT----

upper sequence: GRMZM2G065696_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgacgcctgcgcgacacacacacatagccatcagctttgtctg--tcaatcggataatccgcaattcggttgc-tgaccacgctcccttct--ctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC
|||| |     |  |      ||  ||   | | ||||    |   ||||| |     | |   ||||   ||  | | ||    |  ||     | |||||| |||   |||||||| ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||||| ||||| ||     
gtgatgttcttgatattttggcatttaaa-acctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT----

upper sequence: GRMZM2G065696_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 3'ss of exon 4
--gtgacgcctgcgcg-acacacacacatagccatc---agctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC
  || ||   | |  | |  |    |   ||    |    ||||||||  | |  | |||      |||||           |     | ||| |   | ||||  ||  |||||| || || |||||||| |||||||| || ||| |||| || ||||||||||| ||||||||  | || ||||| ||||||||     
gtgtaacaaattcatggattcttttagtcagttcactgaggctttgtcaattatcctgatg--tgacaattattccaagcttcttttccactttttgtttagGTTCTCCTCTGCTTTGGAAATTCGGTAGCATCAACCCGCTTTCTGTTGCAAGATGAGTTCAACATACAGACAACAAAATGTGACAATTGCATCATT----

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|58029873|gb|CX725300.1|CX725300
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATCGTGC
                            tgctgac  putative branch site (score: 2)
                                  ccacgctcccttctct  CT-rich tract
           ataat  TA-rich tract