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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG

Basic information

species Zea mays
transcript GRMZM2G094255_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 5
cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtc-ccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
|     |||| || ||  || |||| ||||   | |||| |   |||| ||||||||  | | |||| | |    ||  ||||||||  |||| |  |||||| ||||||||||| ||||||||| | ||||| |||||||||||||| |||||||||||||||
cttcttttttttttatcatcgatgccatgctatcttttcagtcatgtatactcctgctatcatcttagacagctattg-atttattcactttgatgaccagCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------cagtcattttgttcattgtcaat-gcgatgcagccctttctgcattgtaaactcctgcagt----taacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                                                                  ||   ||||| || | ||| |||     | ||  | | |     ||||     |||  | |    | | ||||  |  |   |   |   |    |   |   || |||| ||||| |||||||||||  |||||||||| ||||| ||||| |||||||| |  |||
gtagtgtatgctgtttaattacttcattaaagtttagaattttgcctattgagcttctgatgtttccaaatatttt-tttaatgtgaatcatctttcatgcttgttccttttgtctttccctttattcttattatttactaatgaacct-gctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------cagtcattttgttcattgtcaatgcgatgcagccctttctgca----ttgtaaactcctgcagttaacttac-agaaaagtttcatttattcgttttggtcc-cagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                                                                 ||   | | | || | ||| |||    |      |||  ||      ||||     |||  | |    |||  |  || |   | | |     |  |  |    || |||| ||||| |||||||||||  |||||||||| ||||| ||||| |||||||| |  |||
gtagtgtatgttgtttaattacttcattaaactttggaattttgctattgagcctctgatgtttccaaatactctttttaatgtgaatcatctatcatgcttcttgttccttttgtctttccctttattcttattattactaatgaaccctctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
-cagtcattttgttcattg--tcaatgcgatgcagccctttctgcattgtaaactcctg------cagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
    ||  |||| || | |  |        |   |   | ||||  || |    |  |       || | ||  |   |  ||   |  ||||  | ||    |   || |||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||||||||| |||
gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
   || |    || | | |    |  || |||   |||| |  ||   |     | |  ||   ||    |||    | | | | || |||       || |||| || ||||||||||| ||  ||||||| || ||||| ||||||||||||||||| |||
-gttcttcacatttagtattttagt-atccagtt-tttcggtttttctagtgttttc--tttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG

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|76010862|gb|DT938032.1|DT938032
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|12970168|gb|BG266848.1|BG266848
EST:     CTCAAAGAGTTGGCACATACGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|31355338|gb|CD439695.1|CD439695
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76284483|gb|DV024051.1|DV024051
EST:     CAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|94478728|gb|EB707686.1|EB707686
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|71327961|gb|DR800622.1|DR800622
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATACGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|60349510|gb|DN216483.1|DN216483
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGGGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|74232835|gb|DT640749.1|DT640749
EST:     CTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|31664107|gb|CD573287.1|CD573287
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78107717|gb|DV526135.1|DV526135
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                aacttac  putative branch site (score: 2)
                                       ttcgtttt  putative PPT
                         aaaagtttcatttatt  TA-rich tract