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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattattaattgttttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG

Basic information

species Zea mays
transcript GRMZM2G108457_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 4
gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactg-gtttagttgaagactcatgattattaattgt-tttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
|||||||| ||||||||||| |||||||| || | || |||| ||| | || | || || || | | ||||| | | | ||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||
gtgtgagatatttgtgagtttactcacttgttcaatttt---tctttcgtcgaccatgtgattctctgttaacaccagtttattcactttgtttgtagTGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 4
---gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattattaat-----tgtt-ttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
| | |||| ||| | | | | | || | || | || |||| | ||||||| ||| |||| ||| |||||||||| ||||||||||||||||| ||||| ||||| ||||| ||||| ||||
tttctaaaaactattttcaagtgagatagcacc---actgatttacacattg--attaattattcagttattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G34060.1 (Glycine max), 3'ss of exon 4
---gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattattaat-tgtt-ttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
| | | |||| ||| | | || || || | | | || | ||| | | | || | | || |||| ||| |||||||||| ||||||||||||||||| ||||| ||||| ||||| ||||| ||||
tttttctaaactattttcaagtgagatagcaccactgat-ttacacattgtttgattattcaattattggtgcatgattggtaaaatatgtgttattgcagTGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G06820.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgagaga----------tttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattattaattgttttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
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gtgagaaaaaaacattattttttcttaacttgcacaattttttt-cactcaaatttatatccagaata---tagcatggatatcacccttcatatttgcct-gcagTGTTTCATTGTGAGCACAGTCAATGCTTTGCAGACGCCAATGATCAATGCAAGTATG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------gtgtgagagatttgtgagttgactcactttttaagcattccatcttctgtcaatactggtttagttgaagactcatgattatta--attgttttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
||| ||| ||| |||| | |||| || | | || | || ||| ||| | || | ||| | | || | | || |||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| ||||||
gtttgccgcagttatttcatagttgatgtt-gagtttttcttattga-tagctttggaaccttcatatggcatatcc-cactactttcat-gagcatcaatgttaactatggtatgtctgcagTGTTTTATAGTGAGCACAGTTAATGCTTTGCAGACACCAATGATCAATGCGAGCATG

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|149086469|gb|EE176014.2|EE176014
EST:     CTCACAAGTTCATAAAAGATCAGGAGCTACTCTCCTTCATAGATGCTGAG                         TGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCA
genomic: CTCGCAAGTTCATAAAAGATCAGGAGCTACTCTCCTTCATAGATGCTGAGgtgtgagaga ... tgttttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttctgtcaatactggtttagttgaagactcatgattattaattgttttgtagTGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATG
                                      tattaat  putative branch site (score: 2)
 ttgtttt  CT-rich tract
 atgattattaattgtt  TA-rich tract