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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcgacttctcccctccacacagtacactgttcatcaagaaatcccccccgtttaggaatcacagggttcgaaacgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG

Basic information

species Zea mays
transcript GRMZM2G029824_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g02590.4 (Oryza sativa), 3'ss of exon 2
gtaaatcgacttctcccctccacacagtacactgttcatcaagaaatcccccccgtttaggaatcacagggttcgaaacgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG
        | ||||   ||    |||  |    |   | |||  |||   |   | ||  |||| |   | ||         ||||||   ||      ||| ||| ||||||||||||||| |||||||| ||||| ||||||||| |||| || ||||| ||| | ||| |||| |||||   ||||
------gtatttcttttcttt-tacaaaaattcg---aacaaagaattatct--gcttgagaatgatgcgatt--------gttaaccaaagg------cttttacaattgcagTCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG

upper sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G01820.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaatcgacttctcccctccacacagtacactgttcatcaagaaatcccccccgtttaggaatcacagggttcgaa-acgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG
                              | |||| ||       |  |   | |||||   |       | | || |   ||| | || | |||| |            |||||| ||||||||| |||| || |||||||||||| | |||||  |||||||||| ||  | || |||||   ||||
----------------------------gtaatgtt-attgttgctttgcttgcttttagagcttgtcttttccaaacattgattgatcttctggttttg-----------gcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
















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|32824642|gb|CD964364.1|CD964364
EST:     TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAA                         TCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTCGGATCAGTTTGTGTGG
genomic: TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAAgtaaatcgac ... acgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGG
EST: gi|32824901|gb|CD964623.1|CD964623
EST:     TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAA                         TCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTCGGATCAGTTTGTGTGG
genomic: TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAAgtaaatcgac ... acgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGG
EST: gi|76010688|gb|DT937858.1|DT937858
EST:     TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAA                         TCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGG
genomic: TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAAgtaaatcgac ... acgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGG
EST: gi|32791123|gb|CD943359.1|CD943359
EST:     TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAA                         TCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTCGGATCAGTTTGTGTGG
genomic: TCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAAgtaaatcgac ... acgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatcacagggttcgaaacgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG
                     aattaac  putative branch site (score: 2)
                                   ttcttcttctac  putative PPT
                     aattaa  TA-rich tract