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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA

Basic information

species Zea mays
transcript GRMZM2G081812_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||||||||| || || |||| ||  |||   |||| | |     | | 
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
                   | |  || | |   |||| || |  || ||| || ||  |||  |||  | | |||||| |   | |    | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||                                              
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
   ||  |       |     | || | |  |  |  | |||   |  |   | | |         |||  |||| | |  |  |   ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||                                              
--gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttg-------gttggtaatatta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
   ||  |       |     | || | |  |  || | |||   |  ||  |   |  |||    |||  |||| | |  |  |   ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||||||||  |  | | | |   |    |   || | ||    | | |
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.2 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
   ||  |       |     | || | |  |  || | |||   |  ||  |   |  |||    |||  |||| | |  |  |   ||  |  ||||||||||||||||  |||| |||||||| ||||||||||||||||||| |||||||                                              
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgtta--tgatgcttggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG----------------------------------------------

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
---gtatgcttctaaccatca-tctata-tgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
      || |||| |     | || ||  |||||||| ||  |        | |  |||| | |||       | ||| | |    |  ||       |||| |||||||||||||  |||| ||    ||||| ||||||||||||||||||||||||                                              
gtcagttgtttctgaatgcaactccatgctgtctttttgta-atgcagctgtggttatatgttatt-------ttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcttctaaccatcat-ctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtct-tttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
||  | |  ||   | | | ||  |||| |  |      ||| || ||   |   | || || ||      | | | | |||| | |      | | |  |||||||||||||| |||| || |  ||||||||||||||||||||||||||||||                                              
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaac-----acactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------

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|18163216|gb|BM333055.1|BM333055
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATAATAAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
EST: gi|17930578|gb|BM267538.1|BM267538
EST:     CAGCTACGAATGAGGTATATCTGGTGTGGGATAATAAAGCAATGTCAATG                         GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTGTGTTTCTTATGATACTATTATTGTAGTTTCTCAAACAA
                    tgttaat  putative branch site (score: 3)
                                   ttttttgctgtctttt  putative PPT
      atatatgattgaaatg  TA-rich tract