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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactttttgcctcttccatgctttcaattttctgagcaatatacattttgtgacagtagatatcttaattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

Basic information

species Zea mays
transcript GRMZM2G044800_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 2
gtgagaactttttgcctcttcca-----tgctttcaattttctgagcaatatacattttgtgacagtagatatcttaatt-ttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
||  |    |  |||  |||| |     |   | | ||| | ||||||||  |||  |  ||||| |   | |||   |  || |||||||||||| || ||||| ||||||||||| || ||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
gtagggttctgctgctccttcaatcaattatgtactattctgtgagcaattcacacgtcttgacaatgtttttctgcttgattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGTAAGGGTGGCAACCGTTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
gtgagaactttttgcctcttccatgctttca--attttctgagcaatatacattttgtgacagtagatatcttaatt-ttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
||  |    || |||   ||| |||||||    ||| | |||||| |  |||| |  | ||  |   | |||   |  || |||||||||||| || ||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||
gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G30800.1 (Arabidopsis thaliana), 3'ss of exon 2
---gtgagaactttttgcctcttcca-tgctttcaattttctgagcaatatacattttgtgacagtagatatcttaattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
    |    ||   |      ||| | ||||||  |||||    || ||   |  ||| ||    |   |    |  | |   ||||| |||||||| || || || |||| |||||| || || || || || |||||||||| |||||||||||| ||||| ||||| || || || ||||||
gtaattgtcacacctcaaaaattcaactgctttgtatttt---ggctatggtctctttatgcttatgattcaaatgttctatcagCTCGAAGAAATCTGGTAAGGGAAAGAGGCCTGGTAAAGGAGGTAATCGTTTCTGGAAGAACATTGGCCTTGGTTTCAAAACTCCAAGAGAGGCTATTGAA

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 2
--------gtgagaactttttgcctcttccatgctttcaattttctgagcaatatacattttgtgacagtagatatcttaat------------tttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
           |||||||      | | || |  |||  ||  | |||  | | |    |||||| |   |  |||||||||            |||  |||||||||||   ||| || || |||| |||||| ||||| || || ||||||||||||||||||||  | || || ||||| ||||| || |||||||||
atatacctaatagaacttggaatatttcccttttttttcatggt-tgataagtgtgtcatttgtgtcttaaagtatcttaatgagcaattgaactttgcagCTCAAAGAAGGGCGGAAAGGGAAAGAGGCCTGGAAAGGGTGGAAATCGATTCTGGAAGAGCATTGGATTGGGATTTAAGACACCCAGAGATGCAATTGAA

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------gtgagaactttttgcctcttccatgctttcaattttc---tgagcaatatacattttgtgacagtagatatctt---aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
                               ||      ||||| |||     |||   |   |||||   |    |||     |||   |    |   | |  |   ||   |  ||||| |||||||| |  || || |||| |||||| ||||| || ||||| |||||||||||||||||| | || || ||||| ||| | || || ||||||
gtaacagaaaattacgaatacattctcattggtttttgttttttcccttggggatgacattgtttttcccctttttaattcgtttttaccgtttttctctgtgctgaaaacaatccagCTCGAAGAAATCTGCGAAGGGGAAGAGGCCTGGGAAGGGTGGAAACCGGTTCTGGAAGAGCATTGGCTTAGGGTTTAAGACACCCCGAGACGCTATTGAA

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|211021518|gb|FL120655.1|FL120655
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCTGGCAAGGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|149082096|gb|EE171275.2|EE171275
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|60337313|gb|DN204286.1|DN204286
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|211023959|gb|FL120673.1|FL120673
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCTGGCAAGGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|211023956|gb|FL120670.1|FL120670
EST:     ACTGAGAAGGCTTNCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCTGGCAAGGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|211438278|gb|FL120651.1|FL120651
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCTGGCAAGGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|211021531|gb|FL120668.1|FL120668
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCTGGCAAGGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|149004429|gb|EE039065.2|EE039065
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
EST: gi|148984955|gb|EE029619.2|EE029619
EST:     ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAG                         CTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT
genomic: ACTGAGAAGGCTTTCCTCAAGCAGCCAAAGGTTTTCCTCAGgtgagaactt ... aattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaattttctgagcaatatacattttgtgacagtagatatcttaattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA
                                         tcttaat  putative branch site (score: 3)
                                 agtagatatcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaactttttgcctcttccatgctttcaattttctgagcaatatacattttgtgacagtagatatcttaattttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA