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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG

Basic information

species Zea mays
transcript GRMZM2G069008_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 3'ss of exon 2
-atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggaca-atgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
 ||    ||  | ||   |||| ||  |  ||||  ||||   |  |  |     ||| |      ||| || |  || |    |||||||| |||||  || ||||||||||||| |||||||||||||| || |||||||||||||||||||||||||| || ||  |||| || ||||| ||||| ||||||
tattccttgtagcatg--ttgaattagatgtggtcgttgtataggattcaaagtaagcggattttgtgtgtattatattttgagttttgacaatatatccagATTCCAGGAATTGTATTTGCAAGAGGGCCTGCTGTTGCTGTGTTGATTCTTTTGGAGTCTAAAGGGCAAACTTACGCTGTTCTTACAGAACAG

upper sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 3
------------------------------------------------atctactgatgaattccttga-ctttaaattggtatttgtgaggtgta----tagcaccagcaggac-aatgtttagttcatatcatcttttgaca-----gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
                                                 | |  |  | |   |  ||| ||   ||   ||||   |   || ||    |||    || |   | |||| | | |||||    |  | | | |     | ||  |||||||||||| ||||| ||||||||||| || || || ||||||||||| ||  |||| ||  | || || || |||||||| ||||| ||||||
gtatgagatggtttacatacaagtataaatctatgttggcatgttttcctgtgttagtaatggcagtgagctgcgaaccagtatgcatattgtctacttttagacttagtacacctaatgctgatttcattcttttatattaaactaaagcattattagGTTCCAGGTATTGTGTTTGCAAGAGGACCAGCTGTGGCTGTGTTGATGCTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG
















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|91054278|gb|EB164696.1|EB164696
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|29543762|gb|CB604142.1|CB604142
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|148942502|gb|EC887517.2|EC887517
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|91054277|gb|EB164695.1|EB164695
EST:     AACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: AACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|31355362|gb|CD439719.1|CD439719
EST:     TCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|149096585|gb|EE182343.2|EE182343
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
                                     ttttgac  putative branch site (score: 3)
                                            agtatattta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - -ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - caccagc