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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG

Basic information

species Zea mays
transcript GRMZM2G030072_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g22430.2 (Oryza sativa), 3'ss of exon 3
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG----------------------------------------
                                                                               || | |    | |||    ||| || | |     |   |   ||||    ||   | | |  || |   |    | |||  |  ||| |||     |    | ||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||                                        
-------------------------------------------------------------------------------caaggttaaattatttacttagcctgtcaaactacc--aatgtttgagatattaagccct--ttacc-caccccctaatcatcgttttatt-----ttgaaaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT

upper sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g22430.1 (Oryza sativa), 3'ss of exon 3
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG
                                                                               || | |    | |||    ||| || | |     |   |   ||||    ||   | | |  || |   |    | |||  |  ||| |||     |    | ||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||
-------------------------------------------------------------------------------caaggttaaattatttacttagcctgtcaaactacc--aatgtttgagatattaagccct--ttacc-caccccctaatcatcgttttatt-----ttgaaaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAG

upper sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G42180.2 (Glycine max), 3'ss of exon 3
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG
||||    |  |  |   ||| ||  ||  || || | ||     |  || ||||| |        | ||||  || || || | ||     ||| | ||  ||||||      || |||     | || |||| || |   | || | |  ||   |  | | ||  |||| |   || |||   ||||| || |||||||  ||||||||||| || ||||||||||||||||   |||||| ||||
gtaatt--ggcttctggcttgctg-tttatgtgaaatgttcgatttgctgtggtcacttt------actttgtattttttatat-ctgtagtttaagataatctataaa-----ttaagc-----tgtc-tgtcttcctttctcctttgttatc--ctcatgcctt--ttgagttcttgcatt---cagGTAGGCATGGAGACAGAAGGTTTTGCCATTTATGATGCAATGATGCAGTTGAAAAATGAG

upper sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G39570.1 (Glycine max), 3'ss of exon 3
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG
                  |   || |||| | |   || |     |||     |   ||   |  |   |    |||||  ||   || | ||    ||||  | |||| |   | ||  | ||        ||       |||   | |  |    |  | | ||  |||| |   || |||   ||||| || |||||||  ||||||||||| || ||||||||||||||||   ||||||  |||
-----------------gtaattggcttctggct--tactgtttatatgaaaatttttatttgctgtggtcactttattt-tgcattttttatatctgtag--tttaagataa-tctatgaattaagctgcctctctgcctttgtcctttgttatcctcatgcctt--ttgagttcttgcatt---cagGTAGGCATGGAGACTGAAGGTTTTGCCATTTATGATGCAATGATGCAGTTGAAAAACGAG

upper sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0060g02160.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG
                                                                                 |||| |  |   ||| |      ||      | ||  ||||   | | ||       |  |     | ||  |   |  | | |   || |   | | | ||  |||||| ||||||||||  || |||||||| |||||||||||||||||||   | |||| ||||
---------------------------------------------------------------------------------tgttgtgtt--ctagagctattcatttaactttttgggcatcaat-ttatactacattaat-----tttaaccttctgttccatgggttcaaattgtttgttgttcagGTTGGGATGGAGACTGAGGGTTTTGCTATCTATGATGCAATGATGCAGTTAAAAAATGAG

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|32928536|gb|CF033348.1|CF033348
EST:     TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCG                         GTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
genomic: TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCGgtaagcaaga ... tatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
EST: gi|9794785|gb|BE553093.1|BE553093
EST:     TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCG                         GTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
genomic: TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCGgtaagcaaga ... tatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
EST: gi|33103277|gb|CF063237.1|CF063237
EST:     TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCG                         GTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
genomic: TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCGgtaagcaaga ... tatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
EST: gi|32929221|gb|CF034033.1|CF034033
EST:     TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCG                         GTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
genomic: TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCGgtaagcaaga ... tatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
EST: gi|50332076|gb|CO527202.1|CO527202
EST:     TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCG                         GTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG
genomic: TTTATATATACATCAACTCAACTGGAACGGCTCGCGATGATGGTGAACCGgtaagcaaga ... tatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG
                                aattgat  putative branch site (score: 4)
                    aaatagttctttaatt  TA-rich tract