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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

Basic information

species Zea mays
transcript GRMZM2G010085_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
||||||     |||||||   || || ||||| || || |  || | |  ||| |    ||||  || |  |  || |   |   || || ||||||||| |||||||||||||||||||| |||||||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||||
gtatgc-----tgttatgtgcaaatt-gttttctt-ctgaacccatgaatatgtatgt-tgaatatt-tagtgttaatgtgttgatgtcttcagGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
         | |||  |  | || |     || || || || |   ||           ||||  | | | |  | ||  ||  ||  | | |||||||| ||||  ||||||||||| || || |||||||||||||| ||||||||||||||||||||||| || || || |||||||||
--------gtatgtccttttcaaatcgtaattttttctcattctacaatt-------tgtgaagttaaaggttatggttatttggtttcac-agGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatga--accttatgttcctagtactt--ctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
| | |      | ||    |      ||  || |  |||  | |     ||| |   |||||  |  |  | ||  |  || ||    ||     |||||| || |||| ||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||||||||||
gcaagtattcatattg-attgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
----gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
    ||||   |  | ||||||    | | ||   | |   ||||| |   | ||  ||   ||     | ||| |  | || ||| |       |||||| || |||| |||  |||| |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||| ||||||
gtcagtatttcaagtagttatg---gactcagccatctgatttatatctgtacca--aaattattttgttgatggt--tggtgcttttacaa---cagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatga--accttatgttcctagtactt--ctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
||  |     |||||    |      ||  || |  |||  |       ||| |   |||||  |  |  | ||  |  || ||    ||     |||||| || |||| ||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||||||||||
gttagtattcttgttg-attgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
gtatgcgactttgtta-tgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
||  |    | |  || |  | ||   ||   ||||  ||||| |   | |   ||   ||     | ||| |  | || ||| |       |||||| || |||| |||  |||| |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||| ||||||
gtcagtatttctagtagttttgaacacagccatgttatttatatctgtaccc--aaattattttgttgatggt--tggtgcttttacaa---cagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
gtatgcgactttgttatgctaaatttagttttgttgcttataccct--aagcatgaagccatgaaccttatgttcctagtacttctgtgcctcc--agGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
||  || | ||    ||  |   ||   |||  ||    || |     ||   | |    ||  |||  || |   |  |   | | |  | ||  ||||| ||||||| |||| ||||||| || || ||||| ||| | || |||||||||||||||||||||||||| || || ||||| |||
gtgagc-atttctccatttttttttctttttcttttagaatgctagggaattgttatattatttacca-atctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
                                        cttctgt  CT-rich tract
                          ttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT