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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagactagttactgatgccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC

Basic information

species Zea mays
transcript GRMZM2G128971_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 6
cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagac-tagttactgatgccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
||  ||       |   | || |  | | ||    || |   |   |  ||| ||   || |  |  ||| |||   |||||| ||||||| || |||||||||||||| |||||||| |||||| |||| || || || ||||||||||| |||||||||||| | || || ||||| ||||| |||||||| ||||| |
cattttcctacgtagaatgaagtgcagattatcaaatacttttcactattttggagtttatatatttttaatgagctcacatt-ttcttttgctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGGTGGATCAACAACGTACACCATGACATTGGAACCCATGTCATTCATCATC

upper sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G07570.1 (Glycine max), 3'ss of exon 6
--cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagactagttactgat-gccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
      | | | | |    ||||| ||   ||| |   |    |||     || | ||| |  | |  ||  | || ||   ||| ||  |  | |  |  |||| ||||| || ||  | || || || || ||  | || || ||||||||||||||||| |||||||| |||||||| ||||| |||||||| |||||||
ttttcttgagcaagcttctttaatgttt--gtaatgacttggaattggaagttgtcaaaattcagtttttcttcatagctttattcttaatcatgtggac-agGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTACGGATGGATCAATAACATCCACCACGACATTGGAACCCATGTCATTCATCACC

upper sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G29630.1 (Glycine max), 3'ss of exon 6
----cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagactagttactgat-gccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
     || || || | | |   |  || | | |   |  |   |||   |     |  ||| |  | |  ||  | || ||   ||| || ||  | |  || |||| ||||| || ||  | || || || || ||  | || || ||||| ||||||||||||||||| || || ||||| ||||| |||||||| |||||||
cagcaagcttctctatctccaatgcttgtgatgacttggaattagaagtt----atcaaaattcaattttttcttcatagctttattcttattcatgtggat-agGAATGGAGCTACCTTAGGGGTGGCCTTACAACTATTGATCGTGACTATGGATGGATCAACAACATTCACCATGACATTGGAACCCATGTCATTCATCACC

upper sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 3'ss of exon 6
-----cagattatcgaccactgttaattttaaagtactctatccagattcttccttttgaaagtagactagttactgatgccacattgttctttttctatat-tagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
     || | | |    |||  ||  |  |  |||   ||    |||  ||   | |||  ||      | | ||  | ||  ||| || ||||  | | |   |||| |||||||| ||| | ||||| || || ||  | || || ||||||||||||||||| |||||||| ||||| || ||||||||||| || ||||| |
gtatgcaaaatctacttcaccttttgtaatcgagttacctgag-agacactgt-tgttgtgag------aatcacaaacgcttcat-gtactttccccaaacacagGAATGGAGTTACCTGAGAGGAGGGCTCACAACATTAGATCGTGACTACGGATGGATCAATAACATCCACCACGATATTGGAACTCATGTGATACATCATC

upper sequence: GRMZM2G128971_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 3'ss of exon 6
cagattatcgaccactgttaattttaaagtactctatccagat---tcttccttttgaaagtaga-ctagttactgatgccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
   |  ||  |       |  ||  |  || || |  | | ||   |||| ||||| |   || | | |  |  ||     |  |  |  || | | | |  ||||||||||||| ||| | |||||||| || ||  | || || |||||||||| |||||| ||||||||||| || || ||||||||||| || ||||| |
-gtaaaatacatattctctgcttccactgttctttgactacatcgctctttcttttaaggttaaagccaactggtgtgtaaatctcatgattctcccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGATTGATCAATAACATCCATCATGATATTGGAACTCATGTGATACATCATC

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|116815777|gb|EC859087.1|EC859087
EST:     ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG                         GAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
genomic: ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtgatcatta ... tctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
EST: gi|71763576|gb|DR961513.1|DR961513
EST:     ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG                         GAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
genomic: ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtgatcatta ... tctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
EST: gi|60345673|gb|DN212646.1|DN212646
EST:     ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG                         GAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
genomic: ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtgatcatta ... tctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
EST: gi|60357107|gb|DN224080.1|DN224080
EST:     ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAG                         GAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA
genomic: ACTTGCACCATCATGGCCACGAAGACAAGCTTCCCTGGTACCGTGGAAAGgtgatcatta ... tctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttgaaagtagactagttactgatgccacattgttctttttctatattagGAGTGGAGTTATCTGCGTGGAGGACTGACGACGCTCGACCGGGACTACGGATGGATCAACAACATCCATCACGACATCGGAACTCATGTCATCCATCACC
                      tactgat  putative branch site (score: 2)
                                 cattgttctttttct  putative PPT
                                      ttctttttctatatta  TA-rich tract