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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG

Basic information

species Zea mays
transcript GRMZM2G002859_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacac-atattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattac--cgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                          | | ||  | | |||| ||    |   ||| |  |    |    |||||       | ||    ||||   | || |||  |||    || ||   |  |  | |||   | ||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||||||||||||| |||| |||||||||||||||||||
---------------------------------------------------------gtacggcc-ctatcttcccattggacatgtttctaaccataaacatatctttgctggactt----ttgtgggcaaagttggctacactaaacttgtgttcattaacctgctc-aatcagGTGTCAAACAATGGATGGGCAGAAGGTGAATGCAGAGGGAAAGCTGGCTGGTTCCCTTACGACTACATCGAGAAAAGGGACCGTGTGCTTGCAAGTAAAG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacata------aaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                                           || || |        | |||  |     |   | |     |  | |    |||| ||  | |||||  | |||| ||       || |   || |  |   |||||| | |||||||||||||| || ||||||||||  |||||||| |||||||| || |  |  ||||| || | | ||||||| || || ||||| || |
---------------------------------------------------------------------------catatttaaaacaaacttttggttgtggtggtagtggggatggata----accctaaaatcattacatattttaaattgttcccaatatgactctgattggcagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATTGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                    |    |  ||       | |      ||| |||   |  ||| | | |  |||   | || |||  | ||||| ||| ||  ||| |  |  ||| |  | | |              |||||| | |||||||||||||| || ||||||||||  |||||||| |||||||| || |  |  ||||| || | | ||||||| || || ||||| || |
----------------------------------------------------aaaacaaacttt---tggttgtggtgatagtgggaacggattaccttaaaatcatta-catattctaaattgttccc-aatatgact--ctgattgaattgaca--------------cagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATAGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctt-----tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                      |||     |    |    || |||||        || |     |     | | | ||| |||   || |         |   | |      || | |||  |   |  |     || |   |||||  |   || |||||||||||||||||||||||  || ||||||||||||||||| || |  ||||| || | |||||| || || ||||| || ||||
------------------------------------------------------gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcc-tttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtca-tgttatgctgcggccagcttcacacata-ttggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                  ||| ||||  ||||   |||  |   ||||   ||| ||| |  ||| ||   ||| |  | ||         |||||   |   || ||     | |||| ||           |  |  | ||||||| || ||||||||||| |||||||||||||  || || || ||||||||||| |  |  ||  | || || ||||| || || |||||||| ||  
------------------------------------------------cttcactgttcagctgaaaccaa-tgggcacacggttgtttgtcttttttatt--tatttggacca-------tgttgtaatagcgtttcat-----actttatat-----------ttttggt-agGTGTCTAATAATGGATGGGCTGAAGGTGAATGCAAAGGAAAGGCAGGTTGGTTCCCATTTGGATATGTTGAAAAGCGGGAACGGGTTCTTGCAAGCAAGA

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                                   |   ||  ||  |||   ||||  |||    |  | | |  ||    ||  |  || || || |  |   ||||   || |    |       || | ||   |||||||| |||| ||| ||||| |||||||||||||| || ||||| |||||||||||    |  ||||| || | ||| || || || |||||||| ||  
-------------------------------------------------------------------cctttttgca-gtatatcttgcttattcttagcatgtttggatttggtt--atcttttatcccagttcttttacgagatctgttcac---tttctgtgcttggcagGTGTCAAACAGTGGCTGGGCAGAAGGTGAATGCAGAGGAAAAGCAGGTTGGTTCCCAGTTGGATACATAGAAAGACGAGAACGCGTTCTTGCAAGCAAGT

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|71307047|gb|DR789678.1|DR789678
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|149070323|gb|EE158722.2|EE158722
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGGACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|33091909|gb|CF051903.1|CF051903
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|148986436|gb|EE030178.2|EE030178
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|40336986|gb|CK371056.1|CK371056
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|40335185|gb|CK369255.1|CK369255
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|101396723|gb|EB820287.1|EB820287
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|60356623|gb|DN223596.1|DN223596
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|211534621|gb|FL443302.1|FL443302
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|37385184|gb|CF629716.1|CF629716
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|37380473|gb|CF627052.1|CF627052
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|38687511|gb|CK144542.1|CK144542
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
             acttgat  putative branch site (score: 5)
                                        ccctttcct  putative PPT
                         aatttacataaaaaa  TA-rich tract