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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATGATGATGGCAGTTTTTTCAATCTACACAGGATTAATATACAATGAATTTT

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 11
gtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtatt---cccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgc-tgttacatct-ttttttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATGATGATGGCAGTTTTTTCAATCTACACAGGATTAATATACAATGAATTTT
                 | ||||||  || | |||   | |     | ||| |  |  || ||  |  || |  ||     |||||| |    ||| |   ||| ||||| ||    |  |||||| |   ||||     ||   |      || | |   | | || | | ||||  | | |  ||| ||| ||||  ||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||| | ||||||||||| |||||||||||||||||||||||||
-----------------gtttgcatactggt-catcattttactattgtgttgacaatcattttgaggactttgttct---ttggaatatgtagtagtgatcccaaagagtttagagc--aagtattt---atattctgaaagccccaaaaatttaca---tatgtgataaagctgtatctgatgtctgtttcttattgcagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGCTATGTAATTATAATGATGGCACTCTTTTCAATCTATACAGGATTAATATACAATGAATTTT

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatct--ttttttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATGATGATGGCAGTTTTTTCAATCTACACAGGATTAATATACAATGAATTTT
                                                                                         |      || |  |||| |   |||        ||||    || |      || ||   | | | || ||||   | |   |  ||   |    |  ||  | |  |||||||||||| || || ||||| |||   ||||||||||||||||| ||| |||||||| || | || ||||| ||||| |||||||| ||||| || || |
-----------------------------------------------------------------------------------------cttgacgtttctaaagatcagatta-------gtctgttgcattttgatgttttgt---gcttacaagttctagatgctaacctcttcaatcgttgcttcctgacaacagAAACTTGGGGATATTATGGAAATGGCTTTTGGTGGGCGTTATGTCATTTTGATGATGTCACTCTTCTCAATATACACTGGATTAATCTACAACGAGTTCT

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 11
gtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaat-aatttctttgttcatgctgctgttacatctttttttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATGATGATGGCAGTTTTTTCAATCTACACAGGATTAATATACAATGAATTTT
                                                                                               ||| ||    |  |||| | |      | |      |  |  |  |||  |||| |  |  || | || ||||| |||  |  |  || ||| || |   |||||||| |||||||| ||||||||||  ||||||||||||||||| ||||||||||||||| | || ||||| ||||||||||| ||||| |||||||| |
-----------------------------------------------------------------------------------------------atttccttgtacattttgagtcttagctttacttcttaaccaattttcagtttgatggttgatctattagttca-gct--tacttgatttttgttgactgcagAAACTAGGAGACATCATGGAGATGACTTTTGGTGGGCGTTATGTGATTATGATGATGGCACTGTTCTCAATATACACAGGATTGATATATAATGAATTCT

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|32929086|gb|CF033898.1|CF033898
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929323|gb|CF034135.1|CF034135
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929184|gb|CF033996.1|CF033996
EST:     TAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGCGGGCGTTATGTAATTATG
genomic: TAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32930632|gb|CF035444.1|CF035444
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929163|gb|CF033975.1|CF033975
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32928488|gb|CF033300.1|CF033300
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATGATGATGGCAGTTTTTTCAATCTACACAGGATTAATATACAATGAATTTT
     tgttaat  putative branch site (score: 3)
                                  ttacatcttttttt  putative PPT
       ttaataatttctttgt  TA-rich tract