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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 15
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
|||||| ||  ||  |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| ||||| || |||||||||||||| |||||||||||||| ||||||||||||||  ||||| | || || ||||| || ||| ||
gttagttttgatgactccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCCTAGTTACTGGATGCAGACTCTTTTCGGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
|||||| ||  ||| |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| ||||| || |||||||||||||| || ||||||||||| ||||||||||||||  ||||||| || || ||||| || ||| ||
gttagttttgatggctccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
--gtta-gtattcttggtt----ttttttaccctctacttgttcttttcccgttgctc----taacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
  || | || || |   ||    | || |      |  |   || | | | |||| ||    | | | |    | |  |||| || |       |   | |||||||||||||| || ||||| ||||||||||  || | |||||||||||||||||| ||| ||||     |||||   |||||||| || || |   ||
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttc--tgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
-gttag-tattcttggtttt--ttttaccct--ctacttgttcttttcccgttgctctaac-----gctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
 || |  | || |   || |  | |||   |   ||||      | |    ||| ||   |     |||    | || |||| || |       |  || ||||||||||| || || ||||| ||||||||||  || | |||||||||||||||||| ||| ||||     |||||   ||||| || || || |   ||
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttc--tgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 16
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaa-----cgagatcagG-TGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
||  || | ||    ||||  |||      ||||   |  |       || ||        |  ||||   || | | |||      |  | | | | |||| ||| || || || |||||||| || |        |||||||||||||||||||||||||||    ||||| || | || || || || |   ||
gtatgtctcctca--ttttcctactaaaaccttgccttcattatacatctatacttaaatcaatatttaaatttggaaaaattttctctcgttaaagCTGGAGCCCAGATGCAATCGTCTTCAATTCTTCCTTTGTGTATGGAACTCCTAGCTACTGGATGCAGCACTTTTTCAGCAACTCCAGTGGAGCGACTCTT

upper sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
lower sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
-------gttagtattcttggttttttttaccctctacttgttcttt----tcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT
       | |     || |  | |   |        || | |   ||    |   |  |     | |||| ||  |   |   | |        | || ||| |||||||| || || ||||||||||||||||||||||| ||||| || || ||||||||| | ||     |||||    | || | |||||||    | 
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaaac--tagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

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|211495379|gb|FL350690.1|FL350690
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211098336|gb|FL317177.1|FL317177
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211146564|gb|FL325013.1|FL325013
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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