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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttagatcatttatggttcatacataattgtttctgtaattgatttatatatggtttagtattgtctttggtattcatgttcttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT

Basic information

species Zea mays
transcript GRMZM2G056975_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------ttgttttagatcatttatg-gttcatacataat--tgtttctgtaattg---------atttatatatggtttagtattgtcttt--ggtattcatgttcttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
                                                          ||||| |   || |||  | || || ||||  || |   | ||  |          ||||  | ||| ||| |||| | |||   |||||||||   |||||||   | |||||||||||||  | |||||  |||||||||||||||||||| ||||||||||||||||| | || |||||||| |||||||||||||| ||||||||||
gtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATCTTATACACCATGTCTTGGCCAGACAGAATCTATTGCTCAGAGGTCACCT

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 9
---ttgttttagatcatttatggttcatacataattgtttctgtaattgatttatatatggtttagtattgtctttggtattcatgttcttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
   |||| |   || |   |  |   ||| |  |  |       |  | ||| |    || || |  ||| |||    || | |  || ||   |  | | ||||||||||||| || || |||||||| ||||| |||||||| || |||||| | || || ||||||||||| || || || ||||| ||||| | ||| |
aacttgtgtataataaagaaaagggtatagaagaaagaagaaaaagatcattaaccattgtttaatcattatct--aatactaa-attatttcttgattccagGATTCATCTGTTCTTGCACAGTTGGGGTGGCCTGATATGCGTTTGCCAATCCTCTATACATTATCATGGCCTGACAGGATTTATTGTTCTGAAGACACTT

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 9
--ttgttttagatcatttatggttcatacataattgtttctgtaattgatttatatatggtttagtattgtctttggtattcatgttcttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
   |  | || |  ||  |  |   || || |           |||    ||| | || ||| |  ||  | | |  || | |  |  ||   |  | | ||||||||||||| || || || ||||| ||||| |||||||| || |||||| | || || ||||||||||| || || || ||||| ||||| ||||| |
aacttgtgtataatatagaaagggtat-caaagaaaggagaaaaatatcattaaacattgttaatcatattatctaatactaa-atcatttcttgattccagGATTCATCTGTTCTTGCACAATTGGGGTGGCCTGATATGCGTTTGCCAATCCTCTATACATTATCATGGCCTGACAGGATTTATTGTTCTGAAGTCACTT

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgttttagatcatttatggttcatacataattgtttctgtaattgatttatatatggtttagtattgtctttggtattcatgttc-ttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
               | | | | | |||| | |   |   | |||  |||     |  |  |  | |  || |   |    | ||  || ||||| || ||||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||  | |||||| | |||||||| |||||| |   ||| ||||| || || |
--------------gtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccac-agGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT

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|16379495|gb|BI992983.1|BI992983
EST:     ACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: ACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|14244555|gb|BG840684.2|BG840684
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACNCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|31362671|gb|CD447028.1|CD447028
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATAGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|14206809|gb|BG840487.1|BG840487
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCT
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCT
EST: gi|84970217|gb|DW468567.1|DW468567
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|71445034|gb|DR826084.1|DR826084
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|86474441|gb|DY240811.1|DY240811
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
EST: gi|32798103|gb|CD950339.1|CD950339
EST:     AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAG                         GATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC
genomic: AGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagcccta ... gttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttatatatggtttagtattgtctttggtattcatgttcttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
 aattgat  putative branch site (score: 4)
                                      ttcttctgttctact  putative PPT
             tttagtatt  TA-rich tract