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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC

Basic information

species Zea mays
transcript GRMZM2G006130_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
|||||| ||  ||| |   |  |   || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| || || || ||||||||||| || || ||||||||||| ||||||||||||||  ||||||| || || |||||||| ||| | 
gttagttttgatggctccatggt-ttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 15
gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
|||||| ||  ||  |   |  |   || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| || || || ||||||||||| || |||||||||||||| ||||||||||||||  ||||| | || || |||||||| ||| | 
gttagttttgatgactccatggt-ttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCCTAGTTACTGGATGCAGACTCTTTTCGGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
---------gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctct-aacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
         |||   |||     | || |  |      ||  |  | |      ||| ||||  | | |    | |  |||| || |       |   | |||||||||||||| || || || ||||||||||  |||| |||||||||||||||||| ||| ||||     |||||   |||||||| || || |   | 
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttc--tgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
--------gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctct--aacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
        |||   | |  |  | ||    |     |||     | |      ||| |||   |  |||    | || |||| || |       |  || ||||||||||| || || || || ||||||||||  |||| |||||||||||||||||| ||| ||||     |||||   ||||| || || || |   | 
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttc--tgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 16
gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatc-----agGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
||  || | ||   |||  |  ||    ||     |  || | |   |   || |     | ||  ||   ||| ||| ||       ||     || |||| ||| || || ||||||||||| || |        |||||||||||||||||||||||||||    ||||| || | || || || || |   | 
gtatgtctcctcattttcctactaaaaccttgccttcattatacatctatacttaaat--caatatttaaatttggaaaaattttctctcgttaaagCTGGAGCCCAGATGCAATCGTCTTCAATTCTTCCTTTGTGTATGGAACTCCTAGCTACTGGATGCAGCACTTTTTCAGCAACTCCAGTGGAGCGACTCTT

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|67030289|gb|CO459038.1|CO459038
EST:     GTTCAGATGGCA-GTTACGCAC-ACTCTTCGTGA-CGACA-TGAC-AAAC                         GTG-AACCCGGACG-TATCGTCTTCA-CTCCTG-CAGCACTATG-AACTC-
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|211495379|gb|FL350690.1|FL350690
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|32843955|gb|CD983636.1|CD983636
EST:     GTTCAGATGGCAAGTTACGCACCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
EST: gi|211146564|gb|FL325013.1|FL325013
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC
            ctctaac  putative branch site (score: 2)
                            attttgttt  TA-rich tract