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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaactgcacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 8
gtgcggacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaactgcacatgactgatattcgtgtctgtt---ctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA
                                             ||||||  ||    |||    ||||| || |   ||    | | |   |    || |||||   | ||||   || | |||  || ||  |||||||| || || || |||||||||||||||   |||||||||||| |||||||    |||||||| || |||||||||||||||||   |||||||||||  |
---------------------------------------------gtgtgcttctctttatgctatatatttgtttgcatttcttttagttgctatgatgagtgca-caggaaaaccaattattat--tcatggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGGGCAAAGAAAGAAGAGGGGAATGCATTGTTCAAGCTGGGCAAATATGTCA

upper sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 7
gtgcggacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaactgcacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA
                                | |  | |  | ||| | || || |  ||   |  ||||  | | |||| | || | |||| ||   |  || || |||||| || | |  ||   ||  |  ||||| ||||| ||||||||  |||| |   |||||||||||||||| ||||| ||||| || || ||||||||||| || || ||    ||||||||||  |
-----------------------------gtgagagaactatcatgttttcatcttcttat---ttttatt--tttttgtttttaaactttgaactaatttgaaatgtaaaattaattactgaaaa--tgggatgcagGAAAAGGAATCGTGGGATCTGAATACGCAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCTTTATTTAAGGTTGGCAAATATGAAA

upper sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 7
gtgcggacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaactgcacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA
                          ||    || | |  ||  | |   ||  | | | |   |  ||||  | | || | |||||  |||| ||   |  || || |||| | || | |  ||  | |  |  ||||| ||||| ||||||||  |||| |   |||||||||||||||| ||||| ||||| || || ||||||||||| || || ||    ||||||||||  |
-------------------------gtgagagaagtgagagaattat---catgttctcgtc-ttcttatt--tttttggtttaaatt-ttgaactaatttgaaatgtaaaactaattactgaaaa-tggggatgcagGAAAAGGAATCGTGGGATCTGAATACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAA

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|32931241|gb|CF036053.1|CF036053
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211292816|gb|FL187030.1|FL187030
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211294948|gb|FL187036.1|FL187036
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|5901160|gb|AW042260.1|AW042260
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|32936507|gb|CF041326.1|CF041326
EST:     CCCCTAACAGCCCAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|33094682|gb|CF054676.1|CF054676
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|71596242|gb|DR906993.1|DR906993
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211292817|gb|FL187031.1|FL187031
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAATAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211294944|gb|FL187032.1|FL187032
EST:     CACCTAACAGCACAGTGATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|33094689|gb|CF054683.1|CF054683
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGGACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|32934317|gb|CF039129.1|CF039129
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|32935304|gb|CF040116.1|CF040116
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|33091320|gb|CF051314.1|CF051314
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211292815|gb|FL187029.1|FL187029
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211062769|gb|FL037852.1|FL037852
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATG
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATG
EST: gi|211294946|gb|FL187034.1|FL187034
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
EST: gi|211294949|gb|FL187037.1|FL187037
EST:     CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAG                         GACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT
genomic: CACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacat ... tgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA
                                          tcttgtc  CT-rich tract
                         aaaattgatcaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaactgcacatgactgatattcgtgtctgttctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacagGACAAGGAGTCGTGGGACTTGAACAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA