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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC

Basic information

species Zea mays
transcript GRMZM2G010202_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 4
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
|| ||  ||||||||  |    || |     |||     |  |||       || | | || ||    | |   | ||  |   |||  || ||   || |||||||| |||||| ||||    || || |||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||
gtaggcacttatgttgct---gctatagtttgttgccactgagtt------cttaaatgatttagtgtagtatataagcttacctga--ttcatacaatcttagGCAACACTAAGCTGCATGTGGAACTTGAAGAGCTGGTTGCAAGATTTGTTGGCAAGCCTGCAGCTATTCTTTTTGGCATGGGTTATGTGACGAACTCTGC

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 4
gtcggtgcttatgtttatcaaactgtgtca-cgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
    |  |  | | | |  | |  ||  || || | ||  |       ||  ||   |||| |     |  ||  |    || ||| | ||  ||  ||| |||||||| |||||| ||||    || || ||||| || ||||||||||||||||| ||||||||||||||||| || |||||||| |||||||| ||||||||
---cgcaccaaagatcaaaagaaggtaacaacgctataaatttaaatcgtaattattgtaaaagcaagagcttactgcagctaatttatttcaat--gatgttagGCAACACTAAGCTGCATGTGGAACTTGAAGAACTGGTTGCAAGATTTGTTGGCAAGCCTGCAGCTATTCTCTTCGGCATGGGTTATGTGACGAACTCTGC

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 4
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagta--atatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
|| ||| ||  |  ||   |               |  | |  |||  || || || |   || | ||  |    |||    ||| || |  || ||  ||   ||| |  |||  | | |||   ||  | || |||  ||||||||  |||||||| ||||| || |||||  ||||||| |||||||||||||||||||||||
gtaggtactattagtttgtatttcagccattaaaatgtgaattttgtttgtttacatttgcatgtgtcttatcatgtttccttgaatgtggcttttccaat---agGAACAACTGTGCTTCACCTTGAATTGGAGGAGTGTGTTGCAAACTTTGTTGGGAAGCCAGCTGCTATAGTTTTTGGTATGGGCTATGTGACAAACTCTGC

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 4
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagta---atatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
|| |||  |  |  ||   |  |   |||   |   | || | ||   | ||||   |    || | ||  |    |||    ||| || |  || ||  ||   ||| |  |||    | |||   || || || |||  |||||||| ||||||||| ||||| || |||||  ||||||| |||||||||||||| ||||||||
gtaggtattattagtttgtattcca-gtcgt-taaaatgtggttttttttgtttacatttgcatgtgtcttatcatgtttccttgaatgtggcttttccaat---agGGACAACTGCACTTCACCTTGAACTGGAGGAGTGTGTTGCAAAATTTGTTGGGAAGCCAGCTGCTATAGTTTTTGGTATGGGCTATGTGACGAACTCTGC

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 4
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
         ||||||| |      |   |   |||     |||| |   | |||||  || ||      ||   |||     | | |    ||| |||  | |||||  || |  ||||| | |||  | || ||   ||||||||  |||||||| |||||||| || ||  | |||||||||||||||||||||||||||||
--------gtatgtttttttcttcgccccctttttcctcaaggtagtccgttttcatgaacatg--ggtatctatta-----actaaaaaatatatga--tcagGCACCACAACATTGCATAAAGAAGTGGAGGAATGTGTTGCAAACTTTGTTGGAAAGCCTGCTGCAATAGTCTTTGGCATGGGCTATGTGACAAACTCTGC

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|26559603|gb|CA831838.1|CA831838
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|19821837|gb|BQ047861.1|BQ047861
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|22935830|gb|BU572105.1|BU572105
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|87151662|gb|DY396451.1|DY396451
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|20300198|gb|BQ163141.1|BQ163141
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         A
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattag-
EST: gi|20300198|gb|BQ163141.1|BQ163141
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         A
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattag-
EST: gi|24934602|gb|CA452820.1|CA452820
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|18964841|gb|BM661241.1|BM661241
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|87152364|gb|DY397153.1|DY397153
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
EST: gi|87156277|gb|DY401066.1|DY401066
EST:     GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAG                         GCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG
genomic: GTCACTGAAGAAATATTCGGCTAGCACGTGCAGTGTTCGAGTTGATGGAGgtcggtgctt ... ctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC
                                       ttttatct  CT-rich tract
      agtaatatatcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgcttatgtttatcaaactgtgtcacgttttacgtaggttgagtggtttcagtaatatatcaaaattcgttagactgattgagttttatctgatattagGCAATACTAAGTTGCACACAGAGCTCGAAGAGCTTGTTGCAAGATTTGTTGGTAAGCCTGCAGCTATTCTTTTTGGCATGGGCTATGTGACAAACTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT