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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtgggttccatcgggcttttatccctagcctaccccaacttgattaggataaaaggctttgttgttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG

Basic information

species Zea mays
transcript GRMZM2G118014_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
acttgtgggttccatcgg--gcttttatccctagcctacccc--aacttgat-taggataaaaggctttgtt--gttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG
    ||   | |  |  |   |||||   || |   |   |   ||||| || |   ||  |   ||||| |  |   |   ||  | ||| | | | | ||  |||||||||||| |||||||||||||||||||| || || ||| | || ||||||||||||||||| |||| ||||||||| |||
----gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgct-atattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG

upper sequence: GRMZM2G118014_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g62640.3 (Oryza sativa), 3'ss of exon 9
acttgtgggttccatcggg--cttttatccctagcctacccc--aacttgat-taggataaaaggctttgtt--gttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG------------------
    ||   | |  |  |   |||||   || |   |   |   ||||| || |   ||  |   ||||| |  |   |   ||  | ||| | | | | ||  |||||||||||| |||||||||||||||||||| || || ||| | || ||||||||||||||||| |||| ||||||||| |||                  
----gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgct-atattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAGGTACATTCTTGCATACCC

upper sequence: GRMZM2G118014_T05 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 9
-acttgtgggttccatcgggcttttatccctagcctacccca--acttgattaggataaaaggctttgttgttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG
 | ||     ||     ||   |    || ||    |    |         |    |   | | |||| | |  |  ||  | |  || |  |||    |||||||||| ||| | ||||| ||||||||||| ||||| ||| |||| || |||| ||||||||| ||       |||||||| 
tagttagaaatttttggggaaataatgccatatatcaatatattgtcctgctgcttttgtatgttttgctttaat--attttgatttgtat-tattattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA

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|71445995|gb|DR827045.1|DR827045
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACTTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|60349355|gb|DN216328.1|DN216328
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|60359397|gb|DN226370.1|DN226370
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|67019925|gb|CO448674.1|CO448674
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|149079347|gb|EE168323.2|EE168323
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|60347948|gb|DN214921.1|DN214921
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|60348227|gb|DN215200.1|DN215200
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
EST: gi|71445994|gb|DR827044.1|DR827044
EST:     AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAA                         TGATCGACTTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT
genomic: AAGTTGCGCCTCTGTGATATATGTGGAGCATTTCTGAGTGTATATGACAAgtaatgcttc ... atctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaggataaaaggctttgttgttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG
                        tgttgat  putative branch site (score: 4)
                                      tgaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtgggttccatcgggcttttatccctagcctaccccaacttgattaggataaaaggctttgttgttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC