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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttcctttattgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC

Basic information

species Zea mays
transcript GRMZM2G142334_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 7
gctttcctttattgtttttatcacatatccgttaagtttctactg-gtggcatctctgttgttagc-tgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
      ||  | |||          || |  ||  |  |  |  | ||  ||||| | |    |   |  | || | |||| |||  || |||    |||||||||||||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||| ||| |||| |||||
--aaaactcaaatgtgaaatatgtgtaacttttgtggatggagggagtatcatctatctgcccaatgtatttatcgatattattttattgtattgtgtgcagAGGTGATAACATCTGCTGAGTTCCACCCTACTCACTGTAATACATTGGCTTATAGTAGCTCAAAGGGCTCCATTCGACTTGTTGACCTGAGGCAGTCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 7
gctttc--ctttattgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
||| |     || | | |    |  ||||      |  ||| ||    |    | | ||| | |  | | |||   ||   | |   |  ||| |  ||||||||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || ||||| || ||||| ||||||||  ||||||| |||||
gctgttagtcttgtggatcaggtatcataaattgaacctttttaaatatattttttttgtagctt-cagttgagctttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 7
gctttcctttattgttttta-tcacatatccgttaagtttctactggtggcatctctgttgttagct---gctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
   |   |    | |  | | |   |  | | ||||  || |  |  |    | | |||   |||||   | |||   ||   | |   |  ||| |  ||||||||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||||||  ||||||| |||||
--gtggatcaggtatcataaattgaaccttctttaaaattatttttctttt-tttttgtgtgtagctttggttgagccttgaccctatatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGCTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 7
---gctttcctttattgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
   |         | |  | |  |  | | |  |||  |   | |||     |   | |     ||   | |||   ||   | |   |  ||| |  ||||||||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || ||||| || || || ||||||||  |||||||||||||
aaagtgaaggaagaataatctgcttccttttttgttttgc--ccactcagttccattttaaaagtattggttgaatcttgaccctaaatattattat-tgcagAGGTTATAACATCAGCAGAATTTCACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATCCGTCTTGTTGACTTGCGGCAATCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 9
gctttcctttat-tgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagt--tattctttggttctatgac-----------atgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
|    ||||  | |  | ||||| ||  ||   || |||         || | |  | |     ||   ||   |   ||| ||| |  | || |||           |||||||||| || ||||| || ||||| |||||||| ||||||||||  || || ||||| || || || || || ||||| ||  |||||||||| || |||||
gtaagccttggtctactgttatctca-gtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCTATAGCAGTTCGAAAGGTTCAATTCGCCTGATTGATCTGCGCCAGTCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 7
gctttcctttattgtttttatc-acatatccg--ttaagtttctactggtggcatctctgttgttagctgctgatagttattct-ttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
 |||   |  |||   | || |    | || |  ||| ||||||  | ||  | |   |||  |||  |  | ||  | ||  | |||  | | | |  ||||||||| ||||| || || ||||| |||||| | || |||||||  || || ||||||||||| || ||||| || || ||| ||||| |||||||||||||
-cttgaatagattaagtatagctgtctttctgatttatgtttctgattgtaacttggttgtattta--tatttattataatattattgaatttgtaat-tgcagAGGTTATAACTTCAGCAGAATTTCATCCTTCCCACTGCAATATGTTAGCATATAGTAGCTCAAAAGGCTCAATCCGTCTTATTGATTTGCGGCAATCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 7
-gctttcctttattgtttttatcacatatccgttaagtttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgaca--tgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
         || || |||   |   ||||   ||  | |  || | |   ||| |   |    |    |   |  | |   | || ||||   |||  |||||| ||||||||||| ||||||||||| ||||| || || ||||  ||||| || |||||||| |||||||| || || ||| ||||| |||| ||||| ||
gatacaaactttttctttacgtaggatatttatttgggt--taattgcaacatgttgttaaccaatcacacgtc-tgaagttatgcttctgaaacacatgcagAAGTGATAACATCCGCTGAATTCCACCCTACACACTGTAATATGTTGGCATACAGTAGCTCAAAGGGCTCAATCCGTCTTATTGATTTGCGACAATCGGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------gctttcctttattgttt--ttatcacatatccgttaagtttcta---ctggtggcatctctgttgt--tagctgctgata----gttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
                                                                                       | | |  | | ||| |   | |  | | ||   ||     |  |   |   ||||||      ||    |  |  |||||    | | || | | |  ||  |    |||||||||||||| ||||| || || ||||||| |||||||||||  || || || ||||||   ||||| || ||||||||  ||||| |||| ||||||||
gtactgcttcttggttttcagttcttcgactcaccccgctccaacgccatcacctctacatgcaccctgtatattcaaacgtgatatgttgttttctgttgatcagtgaggataaatgatttggaacttcatgtcaattggcattcaaaatgaggcaagtaatgatatgagggttttgtgttggccttggttgagcagAGGTGATAACGTCTGCAGAGTTTCATCCTAATCATTGCAATATTTTAGCATACAGTAGCAGCAAGGGATCTATTCGACTCATTGATATGCGCCAATCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 7
-gctttcctttattgtttttatcacatatcc--gttaagt-ttctactggtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
   |     ||  ||  ||    || |  |   || |||| || ||     | || |    || | |  ||  ||   || |  ||  ||| |  |     ||||||||||||||||||| || || |||||| |||||||||| |  || || || ||||||   || || |||||||| ||  | ||| |||| ||||||||
cagtgaggattgatgacttgggaacctcccaaagtcaagtgttatatgaaagtcagccgacttatgatatga-gactattgtattt--gttttg-gttgaacagAGGTGATAACATCTGCAGAGTTTCATCCTTCTCATTGCAACATGTTAGCATACAGTAGCAGCAAAGGGTCCATTCGCCTCATCGATATGCGTCAATCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------------------------------------gctttcctttattgtttttatcacatatccgttaagtt-tctactggtggcatctctgttgt---------tagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
                                                                                            | || | ||  ||    ||   | |   | || ||| |  |  || |   ||  |||  |         || |  ||    |||| |   | | | |  |     ||||||||||||| ||||| || ||||||||| |||||||||||   || || || ||||||   |||||||| ||||||||  ||||| |||| ||||||||
gtattctctcccatgcgtttagctcatcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacagAGGTGATAACGTCTGCAGAGTTCCATCCTTCTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGCTCTATTCGACTCATTGATATGCGTCAATCAGC

upper sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 7
-----gctttcctttattgtttttatca--catatccgttaagtt------tctactggt-----ggcatctctgttgttagctgctgat-----agttattctttggttctatgacat-----------------------gcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
      ||| | |  |||  | | ||||  || | ||   |  |       |||| | ||     |  |||||| |||||| | | | ||     |||   |   || ||  | || ||                        ||||||||||||| ||||| || |||||||||||||||||||||   || || || ||||||   ||||| |||||||||||  ||||| |||| ||||||||
gtattccttccatgcatttatctcatcagccacaaccaccacctcaacatatctattcgtctctagctatctctcttgttaacagttcattaggcagtggattgatgttttgaggatattgggttgggttgggttgggttgaacagAGGTGATAACTTCTGCAGAGTTCCATCCTACTCATTGCAATGTGTTAGCATACAGTAGCAGCAAGGGTTCCATTCGACTCATTGATATGCGTCAATCAGC

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|67016408|gb|CO445157.1|CO445157
EST:     AAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACTG                         AGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGT
genomic: AAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACTGgtataacttc ... tgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGT
EST: gi|6020391|gb|AW065319.1|AW065319
EST:     AAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACTG                         AGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGT
genomic: AAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACTGgtataacttc ... tgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggcatctctgttgttagctgctgatagttattctttggttctatgacatgcagAGGTGATAACATCTGCTGAATTCCATCCTACTCATTGCAATACATTGGCGTATAGTAGCTCTAAGGGCTCCATTCGACTTGTTGATCTGCGGCAATCAGC
                    tgctgat  putative branch site (score: 3)
                         atagttatt  TA-rich tract