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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatgaaaaatttgcagatttttcttgcagaaaggacttcgactcatcaaaatttcaatcaaatcttactattcttatgttgcatttggcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT

Basic information

species Zea mays
transcript GRMZM2G120578_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 8
-------tatgatgaaaaatttgcagatttttcttgcagaaaggacttcgactcatcaaaatttcaatcaaatcttactattcttatgttgcatttggcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT
        || |||    | ||| | | ||  | | ||    | | | | | |       ||   |||    ||||||  |   | | |||   ||  |  ||||||||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||
ctggtctgatcatgtttgacttgaaaacttcacctacattttgtattcccatttg-----atggtaat--gttcttacactatctgttttggcattatctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAGGCTGAGAGCATGTGGTT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 8
tatgatgaaaaatttgcagatttttcttgcaga-----aaggacttcgactcatcaaaatttca--atcaaatcttactattcttatgttgcatttggcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT
        |  |  |||  ||  | ||   |||     |  ||    || || ||||  |||    || |    | ||||||      || | ||||  ||||  ||| ||||| ||||||||||| ||||||||||| ||||| || || ||||| || || ||||| ||||| ||||||||||||   || || ||||||||| |
-----cttactacatgctaatcatactgaaagatgtaaagagataaagattcctcaatttttggtcattatcattaactattacaggattacttttgtaattt--agGTCCTGCCCAGGAACTTGTTGAGAAGCCTTTCTTTGATACAATAGCTAGGGCATTAAGGCCCGGTGGAGTTCTTTGTAATATGGCAGAAAGTATGTGGCT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 9
-tatgat------gaaaaatttgcagatttttcttgcagaaaggacttcgactc-----atcaaaatttcaatcaaatcttact-----attcttatgttg-catttggcat--ttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT
 ||||||      | |||| |    |  | |    |        | || |  |      ||||||| |    ||| |  | |       | ||| | |||  || |    ||  |   ||| |||||||  |  ||||| ||||||||||| || |||||  | |||||||| |||| |||||| || |||||||||||    || || ||||||||| |
gtatgattcatctgcaaaactctttggatatctgagtgattcttattttgtttttctaaatcaaaactcggttcagacttcagctacaaactctcacgttttcactctatataatcatagGTCCTGCTCTTGCGCTTGTTGAGAAGCCTTTCTTCGAGACACTGGCTAGAGCGTTGAAGCCTGGGGGAGTTCTTTGTAACATGGCAGAAAGTATGTGGCT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 8
tatgatgaaaaatttgcagatttttcttgcagaaaggacttcgactcatcaaaatttcaatcaaatcttactattcttatgttgcatttggcatttgc--agGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT
 |   |  |    ||  || | |    | |  | | |  |  || |  |   || |    | |    |||||   ||| | | |  | |     |     ||| |||||||| |||||||| ||||  || ||||||||||| |  || ||||||||| | ||||||||||||||||||||    ||||| || |||||| |
aactttttatgtcttcaaggtgtaatatcccaataag--tgggatttgtggcaaataaggtaattatttacttcccttgtttggtttcttttcctcatttagGTCCTGCTCAAGAACTTGTCGAGAGACCATTTTTTGAGACAACAGCCAGAGCTTTGCGTCCTGGTGGTGTTCTTTGTAACATGGCTGAAAGCATGTGGCT

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|32919151|gb|CF023963.1|CF023963
EST:     TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAG                         GGCCTGCTCAGGAACTTGTGGAGAAGCCNNNNNNNGAGACCATCGCTAGAG
genomic: TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAGgtgagcttat ... gcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAG
EST: gi|32866078|gb|CF005760.1|CF005760
EST:     TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAG                         GGCCTGCTCAGGAAC-TGTGTGAGAAGCCNNNNNNNGAGACCATCGCTAGA
genomic: TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAGgtgagcttat ... gcatttgcagGGCCTGCTCAGGAACTTGTG-GAGAAGCCTTTTTTTGAGACCATCGCTAGA
EST: gi|211227788|gb|FL398706.1|FL398706
EST:     TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAG                         GGCCTGCTCAGGAACTTGTGGAGAAGCCNNNNNNNGAGACCATCGCTAGAG
genomic: TCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAGgtgagcttat ... gcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaaaatttcaatcaaatcttactattcttatgttgcatttggcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT
                   atcttac  putative branch site (score: 3)
     aaaatttcaatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatgaaaaatttgcagatttttcttgcagaaaggacttcgactcatcaaaatttcaatcaaatcttactattcttatgttgcatttggcatttgcagGGCCTGCTCAGGAACTTGTGGAGAAGCCTTTTTTTGAGACCATCGCTAGAGCTTTGAGGCCTGGTGGTGTTCTTTGTAATCAAGCTGAGAGTATGTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA