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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

Basic information

species Zea mays
transcript GRMZM2G006117_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
gtacaagactgggat-taagaattgcttattttaactttgtttagctgctagtg---tactctttgaatgtt---tcttttgtcatgattttaatggaac--ttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
|||| ||  | | || |     |||  |  | |  |    || |  || ||||    || ||| | ||||||   | | |||  |||||||  || |||   ||   |    || ||||||||||| ||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC

upper sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacaagactgggattaagaatt--gcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaat--tttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
   ||||     | || |  | |  | ||||    |  | |||| | |  |||||   |  |    |||| || || |||   |||| ||     || | || ||   ||||||| |||||  | |||||||||||  | |||||  | || || ||||||| |||  |||| |||||||||||||||||||| |||||||| |||||||| |
--gcaagttcttgtttgactaatcagtttatcaccagatagttttg-tcttagtgagatactattgtgttcctgttctcactgttttgat---ttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC

upper sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 6
gtacaagactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttg-aatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
|||  |        || | |||   | ||  |       || | |||   |||||||    | |||| |  |  |||  || | | |       |     |  | | |||||||||||  | || ||||| || || ||||| ||||||||  ||||| |||||||||| |||||||||||||| ||||| || ||| | ||||| || |
gtaagaccacatactttataataaataatgattttgccattaacctgt--gtgtactacaggcaatgatattcctgtattgctgtca-------tgtgcttggtatgcagGAGAGTGATGTGAAATGGGCCTCTCGATGGGATACCTACCTTCTGATGGCCGATGATCAAATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTTC

upper sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
lower sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtacaa-gactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
   |   ||| || |        ||  | |    |||  || |    || ||      | ||||  |  || |  |   |  ||    ||   ||       |  | ||||  || ||||||   ||||| || |||||||||||||||||| ||||||  || || |||||||||||||| || ||  | |||||  | ||||| || |
--gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgagg-----ccttgaccgcatcctgggctgtccttgctttg---ctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC

upper sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------gtacaagactgggattaagaattgcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttg--tcatgattttaa-----tggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
                                                                            | |  || |    |        | || |||  |   |||  |||| |||||  | | | | ||  |   | | |  ||   |    ||     |||         |  | | ||||| ||||| ||||||||||| || |||||||| || ||  |||||||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| || |
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtc-agctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC

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|32929714|gb|CF034526.1|CF034526
EST:     AAGTTGAAGTTGGCAAGGAAATCATATTCACATATGATGTTCGCTTTGAG                         GAGAGTGAGATCAAGTGGGCGTCACGCT
genomic: AAGTTGAAGTTGGCAAGGAAATCATATTCACATATGATGTTCGCTTTGAGgtacaagact ... taattttcagGAGAGTGAGATCAAGTGGGCGTCACGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctttgaatgtttcttttgtcatgattttaatggaacttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
                                          cactaat  putative branch site (score: 2)
                                      cttccact  CT-rich tract
                       atgattttaat  TA-rich tract