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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaaacaccttaattttttactaatatatgcaattagtggctgctctgattgcttgttaaaatacctgttgatgccatattttctgtgacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTCAGCACTTATCACATTTTGGTATCGATTTTTCTTCACTCCAAAAG

Basic information

species Zea mays
transcript GRMZM2G107696_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107696_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 3'ss of exon 4
ttattaaacaccttaattttttactaatatatgcaatt--agtggctgctctgattgcttgttaaaatacctgttgatgccatattttctgtgacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTCAGCACTTATCACATTTTGGTATCGATTTTTCTTCACTCCAAAAG
|  | || || | |    | | |     || |||   |  |||  ||| | |  ||   | | || |||||| || || | |  ||||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||||||||||| |||||||||||||||||||||
tcctaaagcaacctt-cctatcaagggcatgtgctgctgaagttactgttgtt-ttatatttaaatatacctattcatacaagcttttctgtgacagctcagACGTTTTCTCATACCCAGAAGATGATAGCGTTGAAGATCCACTATTAGCGCAGCATTTGTCACATTTTGGTATTGATTTTTCTTCACTCCAAAAG

upper sequence: GRMZM2G107696_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 3'ss of exon 4
---ttattaaacaccttaattttttactaatatatgcaattagt---ggctgctctgattgcttgttaaaatacctgttgatgccatattttctgtgacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTCAGCACTTATCACATTTTGGTATCGATTTTTCTTCACTCCAAAAG
    || |  |  | |  |  ||| |  ||   ||||||||  |   |     | |  ||  ||  |    ||  | |  |||  |||||    ||| |||||||||||||||||| || || || ||||||||||||   || || ||  |||| ||||| ||  ||  ||||||||| |||||||| ||| | || |||
tgcctagtgtagtcttcgaagtttgatcaa-gcatgcaattgattttgaaaattttattttatttctgtggtaa-tctgaatggtatatt----gtggcagctcagATGTTTTCTCTTATCCGGAGGATGATAGTGTTTTGGACCCCCTTCTAGCACAGCATTTGGCATTTTTTGGTATTGATTTTTCATCATTACAGAAG
















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|32823272|gb|CD962994.1|CD962994
EST:     CCCTCTTGCGGCGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATC
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATC
EST: gi|32934870|gb|CF039682.1|CF039682
EST:     CCCTCTTGCGGTGAAGCTTGGAATAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACC
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACC
EST: gi|116815278|gb|EC858437.1|EC858437
EST:     CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
EST: gi|149014868|gb|EE044579.2|EE044579
EST:     CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACCCTGAAGATG
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACCCTGAAGATG
EST: gi|211413392|gb|FL397573.1|FL397573
EST:     CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
EST: gi|76924845|gb|DV170158.1|DV170158
EST:     CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTC
EST: gi|32929603|gb|CF034415.1|CF034415
EST:     CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAG                         ATGTTTTCTCGT
genomic: CCCTCTTGCGGTGAAGCTTGGAACAATTACTGCTGATTTGGAAGCGGCAGgtaattgtac ... gacagctcagATGTTTTCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctgattgcttgttaaaatacctgttgatgccatattttctgtgacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTCAGCACTTATCACATTTTGGTATCGATTTTTCTTCACTCCAAAAG
                        tgttgat  putative branch site (score: 4)
           ttgttaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaaacaccttaattttttactaatatatgcaattagtggctgctctgattgcttgttaaaatacctgttgatgccatattttctgtgacagctcagATGTTTTCTCGTACCCTGAAGATGATAGTGTTGAAGATCCGCTATTAGCTCAGCACTTATCACATTTTGGTATCGATTTTTCTTCACTCCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA