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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC

Basic information

species Zea mays
transcript GRMZM2G061783_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgctagaggctaatat--aacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
|||  ||    |   |  | |    |   |||   |||| ||   || ||    |||||| ||||  | |   | | || ||| |||| | ||| ||| |||||||| || |||||||||||||| |||||  ||||||| ||||| |||||||| || || ||||| ||||| || | | | |||||||||||
gtatgatgctgtttgtttatagccacaagcaatctatttattctcttatcaacttgctaggggctggtttctgatagctgaatctgtttctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
-------gtactatataatgcttacaaataggctcccaaa---aaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
       | | | | |  || ||    ||||      |||   | |     |  | || ||||  ||||       |||||     | |   | || |  ||   | || |||||||| ||||| |||||||| ||||||||||| |||||||||||||| || || ||   ||| || ||||||||  | ||| |||||||
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttc--agAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G37310.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------gtactatataatgcttacaaataggctcccaaa---aaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                                                 | | | | |  ||  ||   ||||      |||   | |     |  |  | ||||  ||||       |||||     | |   | || |  ||  || ||||||||||| ||||| |||||||| ||||||||||| |||||||||||||| || || || |  || || |||||||   | ||| |||||||
gtatgatatgacaatattccaaacatgttctgaactgaatgtctacaagttcatcttgaaatgttggattttttgttgtctattgatagtgagtaaaatctacaacaaataagactactgatagctacttctctatatattttttcatcctatttc--agAAGGTATGAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTGCCAAGTATTTTGAAAAGATAGAATCATGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g00300.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtactatataatgcttacaaataggctcccaaaaaatttctttcgttt---tctgagtgctagaggctaata-taacaccta-------------aatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                      | |   |    ||   | |   | ||  ||  |||    || ||     | |||| | |  ||   | || |||  | |              ||||   |  | || ||| |||||||| || |||||||||||||| || |||||||| |||||||||||||| || || || || || ||||||||||   | ||| | |||||
gtatacccttaaattcaaaatgagttggtccaactcctataggagttcagaatgaatcctatttgtaacagtatgagagatgtagaacactactaatgcttttttccccgtctctaattcaat-tgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

upper sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g00280.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------gtactatataatgcttacaaataggctcccaaaaaatttctttcgttttctgagtgcta--gaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                  | |||||  |       |   |  ||  |   ||   | |      |   ||   |||   | |||  |    |  ||  | ||     | || ||| |||||||| || |||||||||||||| || |||||||| |||||||||||||| || || || || || ||||||||||   | ||| | |||||
gtatacctttaaattcaaaatgaattggtccaactcctataggagttcagaatgaatcctatctgtaacagtataagagatgtagaacactactaatgctttttccccgtctctaattcaattgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC

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|50336497|gb|CO531623.1|CO531623
EST:     GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAG                         GTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT
genomic: GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT
EST: gi|60357389|gb|DN224362.1|DN224362
EST:     GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAG                         GTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT
genomic: GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT
EST: gi|60353651|gb|DN220624.1|DN220624
EST:     GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAG                         GTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT
genomic: GCAGAATGTAAACATCTTGATACATCTGGACGTTAGTAAAGCACTTAAAGgtactatata ... tgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
                                    acctaaa  putative branch site (score: 3)
                           taatataaca  TA-rich tract