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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatcgttggagtcaaacaatttctagctgccttaccttttagtgtcatacccaatcgcagatttctgctttgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT

Basic information

species Zea mays
transcript GRMZM2G138676_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 5
caatcgttggagtcaaacaatttctagctgccttaccttttagtgtcatacccaatcgcagattt-ctgct---ttgcattaat--ttatctaatttgtcct-gcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
       |  |||   |   ||  |       | |  | |||     | |    ||     |||  || ||   |    | |||  || |     ||||| | ||||||||||||||| |||||||| |||||||||||  |||||||||||||||||||||| ||||| ||||||||||||
-------tccagttgtatttttctttatgatatcatatcttaagacaaaatttgattatttattaactactaagtcatctaaatcgttgttcctgttgtctttgcagATATGCCGAGCACTTGCTTACATACATAACTGTGTTGGCATCTGCCACCGTGATATAAAACCACAGAATGTTCTT

upper sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 4
caatcgttggagtcaaacaatttctagctgccttaccttttagtgtcatacccaatcgcagatttctgctt-----tgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
 ||  |    ||| ||  | | | |   |  |  || |||||    | ||   | |   ||     || ||     |   ||  ||| ||| ||||   |||||||| ||| | || |||||||||||||||||||||||||| || || || ||||| |||||||| |||||  | |||
-aaagg--aaagtaaagtattgtgtgatttac--acattttaaatccctattaatttctagtccattgattatttatttcttcttttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

upper sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 5
caatcgttggagtcaaacaatttctagctgccttacctt---ttagtgtca--tacccaatcgcagatttctgctttgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
          ||| |   | | | |   |  || |  ||   |   | | |  | |    ||   ||||  |  |||   ||  ||| ||| ||||   |||||||| ||| | || |||||||||||||||||||||||||| || || || ||||| |||||||| |||||  | |||
---gaaggaaagtaaggtattgtgtgatttactcattttaaatccctattaatttcttgttcattgattatttatttc--ttcttttctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

upper sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 4
caatcgttggagtcaaacaatttctagctgccttaccttttagtgtcatacccaatcgcagatttctgctttgc-attaatt--tatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
 ||        ||     | ||| |  |||  | |   ||  ||     |    ||    ||||| |  |     | |||||  | ||| | |     || |||| ||| |||||||||| ||||||||||| |||||||| || || |||||||| ||||| || |||||  | |||
-aaaaacatatgtagcttattttatcactg--taagggttatgtactggagttgataattgatttatcatgcattactaattattctcttactctggttgtagATCTGCAGAGCGCTTGCGTATATACATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT

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|211037863|gb|FK972663.1|FK972663
EST:     GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAG                         ATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGT
genomic: GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAGgtctgccttg ... tgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGT
EST: gi|6095487|gb|AW120154.1|AW120154
EST:     GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAG                         ATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGT
genomic: GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAGgtctgccttg ... tgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGT
EST: gi|71322558|gb|DR797956.1|DR797956
EST:     GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAG                         ATATGCCGAGCGCTTGCTTATATACATAAC
genomic: GAATGAATCAGCGGATGCCCCTCATTTATGTCAAACTGTACACGTATCAGgtctgccttg ... tgtcctgcagATATGCCGAGCGCTTGCTTATATACATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatacccaatcgcagatttctgctttgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
                                     atctaat  putative branch site (score: 3)
                                           tttgtcct  CT-rich tract
                        tttgcattaatttatc  TA-rich tract