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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 8
acgactccaccttgtgtggttggctgggtca--agtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgta-attatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
           || ||||||| |||   ||     |   ||   ||| ||  |   ||  || ||  ||      | |  |  |  | |  | |  | ||||||| ||||||||||||||||||||||| || |||||  | ||||||||||||||||||||||| ||||| || ||||| ||||||
---ttgttgggttttgtggtttgctttttctttgattcattcctcgtgaacttgtgttttcatggtgctcagttgtaattgcttacataaaactattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 8
acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttcctt-cacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
      | | | | ||| |         | |    | | |  | |   |   |    |||     | || ||  |         |   ||||| |    ||||||||||||||||||||||||| || || |||||  ||||||  ||||||||||| ||||| |||||||||||||| ||| ||
-atttactagcatttgttgaccttaattttatacttttctcaccttttatcactcaacacttattcttgctcactactttttactttatattttttcaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 8
---acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaag-ggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
   | |    ||  || |||| |    |  |      || || | | |||| | |    | |    |   ||||  ||  ||  ||    || |||   || |||||||||| |||||||||||||| || || |||||  |||||   ||||||||||| ||||| ||||| |||||||| ||| ||
aaaatgttaacaagttctgtgatctcttctgcttgccctgttat-cataaatgctgtgactcttctgatttgttatttttacttctt---tttttttcctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
------acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
      | |     |  || |||| |    || |      || || | |||||| | |    | |      ||| |   | |     | |  || ||||  || |||||||||| |||||||||||||| || || |||||  |||||   ||||||||||| ||||| ||||| |||||||| ||| ||
cataaaatgtgaataagttctgtgatctcttgtgcttgccctgttat-cgtaaatgctgtgactc----ttctgatttgttattttttctt-ttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 8
acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaat-tatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
||   ||   | | | |  |         ||  |   | |   || |   |    |   | || |||  | |   |     |    | ||||| |    ||||||||||||||||||||||||| || || |||||  ||||||  ||||||||||| ||||| |||||||| ||||| ||| ||
acttttctcgcgttttta-tcactcaccacatattcttgtcttgttatcctaaaatgctatggtccttattcactactttttactttatatttttccaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 3'ss of exon 8
---acgactccaccttgtgtggttggctgggtc---aagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
   ||   |   |||| | |     ||||| ||   || | |  || | | |   ||| ||| |    ||  |||  ||  ||  ||    ||  |||||| |||||| ||||| |||||||||||||| || || || ||  | |||| |||||||||||| ||||| ||  |||||||||| ||| | 
actactcttttcccttttctctcaagctggttctctaatttttgttagtgcacttgtttcttaaacttggtttgtgactctaaatgc----at--tttctgagcagGTCTTCAGCTCCTGGATGCACTTTTGTGCTGTACGTGTCTTTGCAGAGAGCATTCTGAGATATGGATTGCCACCATCTTTCTTA

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|148969237|gb|EE019991.2|EE019991
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTTTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|60338311|gb|DN205284.1|DN205284
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|211430021|gb|FL445207.1|FL445207
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
genomic: AAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGC
EST: gi|78120130|gb|DV538514.1|DV538514
EST:     TATGCCAGCTACAG-GAGG                         GTTTTCAGTTCCTGGATGCACTTTTGCGCCGTGCGCATATTTGTAGAGAG
genomic: TATGCCAGCTACAGTGA-Ggtacttagtc ... ttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG
                                         ttatttct  CT-rich tract
                                    tgtaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgactccaccttgtgtggttggctgggtcaagtctcttttgcgtaaaagttccttcacaagggcctgttccttgaacggctgtaattatttctgtgcagGTTTTCAGTTCCTGGATGCACTTCTGCGCCGTGCGCATATTTGTAGAGAGCATTCTTAGATACGGTCTGCCACCATCGTTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA