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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatcacattctatttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA

Basic information

species Zea mays
transcript GRMZM2G018837_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
-cttgcttgcttggcgttttattttaacttatta-ataacagaataatcggtgacctatcacattctat--ttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
 ||||| || |      | ||    | || |  |  | | |   | |   | | | | |    |||| |  |  || |   || |  | || | |  | |||||||||||||||||||| |||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||| 
ccttgcgtgttcattactgtaa---agctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctc-tgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 2
cttgcttgcttggcgttttattttaacttattaata----acagaataatcggtgacctatcacattctatttgttgtaaacggtctgtctgt-ctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
  || ||  | ||   || |   |||  | |||||     | ||  ||||  |      |   ||||    ||||| |      | | |   | | |   |||||||| |||||||||||  | |||||||| ||||||||||  || || |||||| |||| || |||||||||||||| 
--tg-ttattagggtattaacactaatatgttaatctgttaaagcttaatttgctgatcaatgcattt--gttgtttttcttcatttattcataccaatttgcagTGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctat---cacattctatttgttgtaaacggtctgtctgtctaccat--gcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
     | |  |    |||  | |||| |||| | | |   | |  |   | |  |||    |   |   |||  | |||  | |   |     |||  |  ||||||| ||||| |||||  | |||||||| ||| |||||| ||| |||||||| || ||||| |||||||||||||| 
----atagggttttatttcttattaa-ttataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatc-acattct------atttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
               ||||||||    ||| | ||||   |   |   ||  |  ||  | |||         |||  | |||  | |   |     ||   |||||||| ||||| |||||  | |||||||| ||| |||||| ||| |||||||| || ||||| |||||||||||||| 
-------aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatcac-attctatttgttgta-aacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
 ||||   |||| |  ||| | ||||     ||  |||     |||     || |||    ||   | || |  || |        | | | || |||||||||| || || |||||  | |||||||||||||||||||  || |||||||| |||||||| |||||||||||||| 
tttgcc--cttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
--------cttgcttgcttggcgttttattttaacttattaat-aacagaataatcggtgacctatcacattctatttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
                    | |  || ||||   |||||||| |      |  ||  || ||| |   ||| | ||||||| ||      |||   | |    |||||||| || ||||||||  | |||||||||||||||||||  || ||||||||||||||||| |||||||| ||||| 
caaacaaaggaatcgaggcagtgggtt-ttttgtattattaattagttccgttttctatgccctgtt--attttgtttgttgaaa------tgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT

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|76937510|gb|DV175167.1|DV175167
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149000276|gb|EE037432.2|EE037432
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149075355|gb|EE163864.2|EE163864
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149014700|gb|EE044372.2|EE044372
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|76910443|gb|DV163876.1|DV163876
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|148956501|gb|EC902338.2|EC902338
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|26557412|gb|CA829647.1|CA829647
EST:     GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAG                         TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGGCGCCCTGATGCCAAGAGGCCGCGGCCTCCGGCTCTGGCCAGgtgaggagcc ... taccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtgacctatcacattctatttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
                                       tctgtct  CT-rich tract
               attctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatcacattctatttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG