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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcagttcctttttccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG

Basic information

species Zea mays
transcript GRMZM2G133226_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 3'ss of exon 5
---gtaaagcagttcct-ttttccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
     |   || || |  |||| | ||||| | |    ||  |   |||| |  |||||| | |||  ||| | |||  |   |||||||||||||||| || |||||||| ||||||||||||||||| |
gtaacatttcattttcagttttgccacatacaatcccattctaaactacatag-ctttctaaccagcagttttgttttgttt-tagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G07030.1 (Glycine max), 3'ss of exon 5
------------------------gtaaagcagttccttttt-ccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
                          | ||  |    | | | ||    |  | |||  ||  |  || ||   |||| || ||  |   || | | | ||    ||| ||| |||||||||| |||||||||||||| |||||||| ||||
gtattccttgtctctctcattccgacacagtggaaattctataccttttttcattgtagttgga--gtgcagtttcttacttatttggcattatgtctttttt-cagGCAAAACTAGTGGCCTTAATAGCTTTGGCCTTATGTGGTGTAATG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G14360.1 (Glycine max), 3'ss of exon 5
---------------------------gtaaagcagttcctttttccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
                             | |  |||    ||||  | | |||  | |  |  || | | ||   ||||  |  |  | | |  | | | ||    ||| ||| ||||||| || |||||||||||||| |||||||||||||
gttgtattcctatacttctagtctctcacataa-agtgaaattttataccttat--tttcttcccagcctgcattttcttatttgtatggtatcatgtctttttatcagGGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G07120.1 (Glycine max), 3'ss of exon 3
---gtaaagcagttccttttt-ccaacatatagtg-------------ttctttcatcgta-----caaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
   |||   | ||||  | ||  | ||| | ||||             || |||| | |||     ||   |||| || ||  |   || | | | ||    ||| ||| |||||||||| |||||||||||||| |||||||||||||
gtcgtattcctgttctctcttatccacacacagtggaaattctataccttttttccttgtagagttcagtttcttacttatttggcattatgtctttttt-cagGCAAAACTAGTGGCCTTAATAGCTTTGGCCTTATGTGGTGCAATG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G32030.1 (Glycine max), 3'ss of exon 5
---------------------------gtaaagcagttcctttttccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
                             | |  |||    ||||  | | | |  | |||       | | |   ||||  | ||  | | |  | | | ||    ||| ||| ||||||| || |||||||||||||| |||||||||||||
gttgtattcctatacttttactctctcacataa-agtgaaattttataccttcttttcttccaagcctgcatattttcttatttatatggtatcgtgtctttttatcagGGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 3'ss of exon 5
-----gtaaagcagttcctttttccaacatatagtgttctttcat--cgtacaaaat--ctttctgatcagatgttctttttcttcca-------tagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
      |   |   ||   | |||  |  | |  |  ||| |  |  ||| |||| |  ||||||  | | ||||  | ||| |  ||        ||||||||| |||||||||| |||||||||||| |||||| ||||||
gtactattttgttcttatgtcttctcatgtttcattctctatggtaacgttcaaagtttctttctattgatatgtggtatttttctcaattgtctcagGAAAATCCAGTGGCCTCAGTAGCTTTGGCCTTATGTGGAGCAATG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 5
---------gtaaagcagttcctttttccaacatat----agtgttctttca-tcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
           |      ||   ||||  || | |     | ||   | ||| | |    |  ||||||| |   | || | ||||  || |  ||| |||||||||||||| |||||||||||||| |||||||| ||||
gtagaatttccatttttattttattttttaaaaaacttccaatgacatctcagtagcttgatttctttcttagatgctgatattttcttttctcagGGAAATCTAGTGGCCTTAATAGCTTTGGCCTAATGTGGTGTAATG

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|71440135|gb|DR821185.1|DR821185
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|148933234|gb|EC876885.2|EC876885
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|149103657|gb|EE289061.2|EE289061
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|148947033|gb|EC892330.2|EC892330
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|91054598|gb|EB165016.1|EB165016
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
EST: gi|91054599|gb|EB165017.1|EB165017
EST:     TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAG                         GAAAATCTAGTGGCCCTCA-TAGCTTTGGCCTGAT
genomic: TGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaagcagt ... tcttccatagGAAAATCTAGTGGCC-TCAATAGCTTTGGCCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatagGAAAATCTAGTGGCCTCAATAGCTTTGGCCTGATGTGGTGCAATG
                         ttctgat  putative branch site (score: 3)
                                    tgttctttttcttcca  putative PPT
                  aaaatcttt  TA-rich tract